rs372723857

Variant names:

Your query was ambiguous. Multiple possible variants found:

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBP6_Very_Strong

The NM_004260.4(RECQL4):c.2756-8G>T variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000163 in 1,611,492 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Likely benign (★★).

Frequency

Genomes: 𝑓 0.000085 ( 0 hom., cov: 34)

Exomes 𝑓: 0.00017 ( 0 hom. )

Consequence

RECQL4
NM_004260.4 splice_region, intron

Scores

Splicing: ADA: 0.00007043

Clinical Significance

Benign/Likely benign criteria provided, multiple submitters, no conflicts B:6

Conservation

PhyloP100: -1.09

Publications

1 publications found

Variant links:

COSMIC-nc: COSV56741490

Genes affected

RECQL4 (HGNC:9949): (RecQ like helicase 4) The protein encoded by this gene is a DNA helicase that belongs to the RecQ helicase family. DNA helicases unwind double-stranded DNA into single-stranded DNAs and may modulate chromosome segregation. This gene is predominantly expressed in thymus and testis. Mutations in this gene are associated with Rothmund-Thomson, RAPADILINO and Baller-Gerold syndromes. [provided by RefSeq, Jan 2010]

RECQL4 Gene-Disease associations (from GenCC):

Baller-Gerold syndrome
Inheritance: AR Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: PanelApp Australia, G2P, Orphanet
Rothmund-Thomson syndrome
Inheritance: AR Classification: DEFINITIVE Submitted by: ClinGen
Rothmund-Thomson syndrome type 2
Inheritance: AR Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: Labcorp Genetics (formerly Invitae), Orphanet, Genomics England PanelApp, G2P
osteosarcoma
Inheritance: AR Classification: STRONG Submitted by: Genomics England PanelApp
rapadilino syndrome
Inheritance: AR Classification: STRONG, SUPPORTIVE Submitted by: Orphanet, Genomics England PanelApp

RECQL4 links:

ENSG00000265393 (HGNC:):

ENSG00000265393 links:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.8).

BP6

Variant 8-144512779-C-A is Benign according to our data. Variant chr8-144512779-C-A is described in CliVar as Benign/Likely_benign. Clinvar id is 414196.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr8-144512779-C-A is described in CliVar as Benign/Likely_benign. Clinvar id is 414196.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr8-144512779-C-A is described in CliVar as Benign/Likely_benign. Clinvar id is 414196.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr8-144512779-C-A is described in CliVar as Benign/Likely_benign. Clinvar id is 414196.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr8-144512779-C-A is described in CliVar as Benign/Likely_benign. Clinvar id is 414196.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr8-144512779-C-A is described in CliVar as Benign/Likely_benign. Clinvar id is 414196.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr8-144512779-C-A is described in CliVar as Benign/Likely_benign. Clinvar id is 414196.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr8-144512779-C-A is described in CliVar as Benign/Likely_benign. Clinvar id is 414196.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr8-144512779-C-A is described in CliVar as Benign/Likely_benign. Clinvar id is 414196.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr8-144512779-C-A is described in CliVar as Benign/Likely_benign. Clinvar id is 414196.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr8-144512779-C-A is described in CliVar as Benign/Likely_benign. Clinvar id is 414196.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr8-144512779-C-A is described in CliVar as Benign/Likely_benign. Clinvar id is 414196.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr8-144512779-C-A is described in CliVar as Benign/Likely_benign. Clinvar id is 414196.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr8-144512779-C-A is described in CliVar as Benign/Likely_benign. Clinvar id is 414196.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr8-144512779-C-A is described in CliVar as Benign/Likely_benign. Clinvar id is 414196.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr8-144512779-C-A is described in CliVar as Benign/Likely_benign. Clinvar id is 414196.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr8-144512779-C-A is described in CliVar as Benign/Likely_benign. Clinvar id is 414196.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr8-144512779-C-A is described in CliVar as Benign/Likely_benign. Clinvar id is 414196.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr8-144512779-C-A is described in CliVar as Benign/Likely_benign. Clinvar id is 414196.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr8-144512779-C-A is described in CliVar as Benign/Likely_benign. Clinvar id is 414196.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr8-144512779-C-A is described in CliVar as Benign/Likely_benign. Clinvar id is 414196.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr8-144512779-C-A is described in CliVar as Benign/Likely_benign. Clinvar id is 414196.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr8-144512779-C-A is described in CliVar as Benign/Likely_benign. Clinvar id is 414196.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr8-144512779-C-A is described in CliVar as Benign/Likely_benign. Clinvar id is 414196.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr8-144512779-C-A is described in CliVar as Benign/Likely_benign. Clinvar id is 414196.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr8-144512779-C-A is described in CliVar as Benign/Likely_benign. Clinvar id is 414196.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr8-144512779-C-A is described in CliVar as Benign/Likely_benign. Clinvar id is 414196.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr8-144512779-C-A is described in CliVar as Benign/Likely_benign. Clinvar id is 414196.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr8-144512779-C-A is described in CliVar as Benign/Likely_benign. Clinvar id is 414196.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr8-144512779-C-A is described in CliVar as Benign/Likely_benign. Clinvar id is 414196.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr8-144512779-C-A is described in CliVar as Benign/Likely_benign. Clinvar id is 414196.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr8-144512779-C-A is described in CliVar as Benign/Likely_benign. Clinvar id is 414196.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr8-144512779-C-A is described in CliVar as Benign/Likely_benign. Clinvar id is 414196.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr8-144512779-C-A is described in CliVar as Benign/Likely_benign. Clinvar id is 414196.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
RECQL4	NM_004260.4 link	c.2756-8G>T		splice_region_variant, intron_variant	Intron 15 of 20	ENST00000617875.6	NP_004251.4	O94761

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
RECQL4	ENST00000617875.6 link	c.2756-8G>T		splice_region_variant, intron_variant	Intron 15 of 20	1	NM_004260.4	ENSP00000482313.2		O94761

Frequencies

GnomAD3 genomes

AF:

0.0000854

AC:

AN:

152216

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0000654

Gnomad ASJ

AF:

0.00173

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.000207

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00633

Gnomad NFE

AF:

0.0000441

Gnomad OTH

AF:

0.00

GnomAD2 exomes

AF:

0.000237

AC:

AN:

245222

AF XY:

0.000224

show subpopulations

Gnomad AFR exome

AF:

0.00

Gnomad AMR exome

AF:

0.00

Gnomad ASJ exome

AF:

0.00262

Gnomad EAS exome

AF:

0.00

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.000144

Gnomad OTH exome

AF:

0.000168

GnomAD4 exome

AF:

0.000171

AC:

250

AN:

1459158

Hom.:

Cov.:

AF XY:

0.000178

AC XY:

129

AN XY:

725836

show subpopulations

African (AFR)

AF:

0.000149

AC:

AN:

33474

American (AMR)

AF:

0.0000448

AC:

AN:

44614

Ashkenazi Jewish (ASJ)

AF:

0.00306

AC:

AN:

26108

East Asian (EAS)

AF:

0.00

AC:

AN:

39678

South Asian (SAS)

AF:

0.000685

AC:

AN:

86192

European-Finnish (FIN)

AF:

0.00

AC:

AN:

51386

Middle Eastern (MID)

AF:

0.00156

AC:

AN:

5766

European-Non Finnish (NFE)

AF:

0.0000657

AC:

AN:

1111630

Other (OTH)

AF:

0.000365

AC:

AN:

60310

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.489

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.0000853

AC:

AN:

152334

Hom.:

Cov.:

AF XY:

0.000107

AC XY:

AN XY:

74488

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

41582

American (AMR)

AF:

0.0000653

AC:

AN:

15308

Ashkenazi Jewish (ASJ)

AF:

0.00173

AC:

AN:

3472

East Asian (EAS)

AF:

0.00

AC:

AN:

5180

South Asian (SAS)

AF:

0.000207

AC:

AN:

4826

European-Finnish (FIN)

AF:

0.00

AC:

AN:

10622

Middle Eastern (MID)

AF:

0.00680

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0000441

AC:

AN:

68024

Other (OTH)

AF:

0.00

AC:

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.467

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.000425

Hom.:

Bravo

AF:

0.0000982

Asia WGS

AF:

0.000577

AC:

AN:

3478

ClinVar

Significance: Benign/Likely benign

Submissions summary: Benign:6

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Breakthrough Genomics, Breakthrough Genomics

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:not provided

- -

Sep 01, 2024

CeGaT Center for Human Genetics Tuebingen

Significance:Likely benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

RECQL4: BP4 -

Rapadilino syndrome

Benign:1

Feb 01, 2025

KCCC/NGS Laboratory, Kuwait Cancer Control Center

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

Rothmund-Thomson syndrome type 2

Benign:1

Jul 07, 2023

KCCC/NGS Laboratory, Kuwait Cancer Control Center

Significance:Likely benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

Hereditary cancer-predisposing syndrome

Benign:1

Jan 27, 2022

Sema4, Sema4

Significance:Likely benign

Review Status:criteria provided, single submitter

Collection Method:curation

- -

Baller-Gerold syndrome

Benign:1

Jan 13, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.80

CADD

Benign

4.0

(source)

DANN

Benign

0.77

PhyloP100

-1.1

PromoterAI

0.014

Neutral

(source)

Mutation Taster

=100/0

polymorphism

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

dbscSNV1_ADA

Benign

0.000070

dbscSNV1_RF

Benign

0.0020

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

Other links and lift over