Variant chr8-144513211-T-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBP6_Very_Strong

The ENST00000617875.6(RECQL4):c.2463+7A>C variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. 1/1 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Likely benign (★★).

Frequency

Genomes: 𝑓 0.13 ( 0 hom., cov: 20)

Exomes 𝑓: 0.0021 ( 0 hom. )

Failed GnomAD Quality Control

Consequence

RECQL4
ENST00000617875.6 splice_region, intron

Scores

Clinical Significance

Likely benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -3.11

Variant links:

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 links:

(HGNC:):

links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.85).

BP6

Variant 8-144513211-T-G is Benign according to our data. Variant chr8-144513211-T-G is described in ClinVar as [Likely_benign]. Clinvar id is 239732.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr8-144513211-T-G is described in Lovd as [Benign].

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
RECQL4	NM_004260.4 linkuse as main transcript	c.2463+7A>C		splice_region_variant, intron_variant		ENST00000617875.6	NP_004251.4

Ensembl

Gene	Transcript	HGVSc	Effect	TSL	MANE	Protein	Appris
RECQL4	ENST00000617875.6 linkuse as main transcript	c.2463+7A>C	splice_region_variant, intron_variant	1	NM_004260.4	ENSP00000482313	P1
RECQL4	ENST00000621189.4 linkuse as main transcript	c.1392+7A>C	splice_region_variant, intron_variant	1		ENSP00000483145
	ENST00000580385.1 linkuse as main transcript	n.271+374T>G	intron_variant, non_coding_transcript_variant	3
RECQL4	ENST00000534626.6 linkuse as main transcript	c.635-73A>C	intron_variant	5		ENSP00000477457

Frequencies

GnomAD3 genomes

AF:

0.00

AC:

10214

AN:

78408

Hom.:

Cov.:

FAILED QC

Gnomad AFR

AF:

0.167

Gnomad AMI

AF:

0.203

Gnomad AMR

AF:

0.133

Gnomad ASJ

AF:

0.126

Gnomad EAS

AF:

0.0998

Gnomad SAS

AF:

0.0467

Gnomad FIN

AF:

0.106

Gnomad MID

AF:

0.151

Gnomad NFE

AF:

0.121

Gnomad OTH

AF:

0.122

GnomAD3 exomes

AF:

0.00691

AC:

457

AN:

66174

Hom.:

AF XY:

0.00706

AC XY:

251

AN XY:

35568

show subpopulations

Gnomad AFR exome

AF:

0.0204

Gnomad AMR exome

AF:

0.00633

Gnomad ASJ exome

AF:

0.00757

Gnomad EAS exome

AF:

0.0106

Gnomad SAS exome

AF:

0.00246

Gnomad FIN exome

AF:

0.00706

Gnomad NFE exome

AF:

0.00617

Gnomad OTH exome

AF:

0.00566

GnomAD4 exome

Data not reliable, filtered out with message: AS_VQSR

AF:

0.00210

AC:

1896

AN:

901164

Hom.:

Cov.:

AF XY:

0.00225

AC XY:

992

AN XY:

441074

show subpopulations

Gnomad4 AFR exome

AF:

0.00637

Gnomad4 AMR exome

AF:

0.00505

Gnomad4 ASJ exome

AF:

0.00397

Gnomad4 EAS exome

AF:

0.00405

Gnomad4 SAS exome

AF:

0.00383

Gnomad4 FIN exome

AF:

0.00235

Gnomad4 NFE exome

AF:

0.00159

Gnomad4 OTH exome

AF:

0.00266

GnomAD4 genome

Data not reliable, filtered out with message: AS_VQSR

AF:

0.130

AC:

10219

AN:

78438

Hom.:

Cov.:

AF XY:

0.128

AC XY:

4744

AN XY:

36992

show subpopulations

Gnomad4 AFR

AF:

0.167

Gnomad4 AMR

AF:

0.133

Gnomad4 ASJ

AF:

0.126

Gnomad4 EAS

AF:

0.100

Gnomad4 SAS

AF:

0.0468

Gnomad4 FIN

AF:

0.106

Gnomad4 NFE

AF:

0.121

Gnomad4 OTH

AF:

0.125

Alfa

AF:

0.00786

Hom.:

ClinVar

Significance: Likely benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:1

Likely benign, criteria provided, single submitter

not provided

Breakthrough Genomics, Breakthrough Genomics

- -

Baller-Gerold syndrome

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

Labcorp Genetics (formerly Invitae), Labcorp

Nov 09, 2022

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.85

CADD

Benign

0.28

DANN

Benign

0.55

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.050

Details are displayed if max score is > 0.2

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over