Genetic Variant RECQL4:p.Gly1105Asp (chr8-144511990-C-T) – ACMG Classification: Benign (-13 pts)

Variant summary

Our verdict is Benign. The variant received -13 ACMG points: 0P and 13B. BP4_StrongBP6BS1BS2

The NM_004260.4(RECQL4):c.3314G>A(p.Gly1105Asp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00529 in 1,610,530 control chromosomes in the GnomAD database, including 27 homozygotes. In-silico tool predicts a benign outcome for this variant. 10/13 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. G1105R) has been classified as Uncertain significance.

Frequency

Genomes: 𝑓 0.0038 ( 3 hom., cov: 35)

Exomes 𝑓: 0.0054 ( 24 hom. )

Consequence

RECQL4
NM_004260.4 missense

Scores

Clinical Significance

Conflicting classifications of pathogenicity criteria provided, conflicting classifications U:1B:9O:1

Conservation

PhyloP100: 0.183

Publications

13 publications found

Variant links:

COSMIC-nc: COSV56740020

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, SUPPORTIVE Submitted by: Orphanet, G2P
Rothmund-Thomson syndrome
Inheritance: AR Classification: DEFINITIVE Submitted by: ClinGen
Rothmund-Thomson syndrome type 2
Inheritance: AR Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: Genomics England PanelApp, Labcorp Genetics (formerly Invitae), Orphanet, G2P
osteosarcoma
Inheritance: AR Classification: STRONG Submitted by: Genomics England PanelApp
rapadilino syndrome
Inheritance: AR Classification: STRONG, SUPPORTIVE Submitted by: Genomics England PanelApp, Orphanet
congenital heart disease
Inheritance: AD Classification: NO_KNOWN Submitted by: ClinGen

RECQL4 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -13 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.00393191).

BP6

Variant 8-144511990-C-T is Benign according to our data. Variant chr8-144511990-C-T is described in ClinVar as Conflicting_classifications_of_pathogenicity. ClinVar VariationId is 135151.

BS1

Variant frequency is greater than expected in population mid. GnomAdExome4 allele frequency = 0.00544 (7936/1458148) while in subpopulation MID AF = 0.012 (69/5764). AF 95% confidence interval is 0.0097. There are 24 homozygotes in GnomAdExome4. There are 4030 alleles in the male GnomAdExome4 subpopulation. Median coverage is 58. This position passed quality control check.

BS2

High Homozygotes in GnomAd4 at 3 AR gene

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_004260.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
RECQL4	NM_004260.4	MANE Select	c.3314G>A	p.Gly1105Asp	missense	Exon 19 of 21	NP_004251.4	O94761
RECQL4	NM_001413019.1		c.3389G>A	p.Gly1130Asp	missense	Exon 18 of 20	NP_001399948.1
RECQL4	NM_001413036.1		c.3314G>A	p.Gly1105Asp	missense	Exon 19 of 21	NP_001399965.1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
RECQL4	ENST00000617875.6	TSL:1 MANE Select	c.3314G>A	p.Gly1105Asp	missense	Exon 19 of 21	ENSP00000482313.2	O94761
RECQL4	ENST00000621189.4	TSL:1	c.2243G>A	p.Gly748Asp	missense	Exon 18 of 20	ENSP00000483145.1	A0A087X072
RECQL4	ENST00000971710.1		c.3221G>A	p.Gly1074Asp	missense	Exon 19 of 21	ENSP00000641769.1

Frequencies

GnomAD3 genomes

AF:

0.00383

AC:

583

AN:

152264

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00101

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00497

Gnomad ASJ

AF:

0.00374

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00475

Gnomad FIN

AF:

0.000753

Gnomad MID

AF:

0.0127

Gnomad NFE

AF:

0.00594

Gnomad OTH

AF:

0.00621

GnomAD2 exomes

AF:

0.00476

AC:

1156

AN:

243042

AF XY:

0.00506

show subpopulations

Gnomad AFR exome

AF:

0.00108

Gnomad AMR exome

AF:

0.00467

Gnomad ASJ exome

AF:

0.00567

Gnomad EAS exome

AF:

0.00

Gnomad FIN exome

AF:

0.000726

Gnomad NFE exome

AF:

0.00659

Gnomad OTH exome

AF:

0.00441

GnomAD4 exome

AF:

0.00544

AC:

7936

AN:

1458148

Hom.:

Cov.:

AF XY:

0.00556

AC XY:

4030

AN XY:

725292

show subpopulations

African (AFR)

AF:

0.000807

AC:

AN:

33472

American (AMR)

AF:

0.00443

AC:

197

AN:

44476

Ashkenazi Jewish (ASJ)

AF:

0.00594

AC:

155

AN:

26076

East Asian (EAS)

AF:

0.00

AC:

AN:

39660

South Asian (SAS)

AF:

0.00552

AC:

474

AN:

85934

European-Finnish (FIN)

AF:

0.000762

AC:

AN:

51214

Middle Eastern (MID)

AF:

0.0120

AC:

AN:

5764

European-Non Finnish (NFE)

AF:

0.00597

AC:

6637

AN:

1111278

Other (OTH)

AF:

0.00561

AC:

338

AN:

60274

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.485

Heterozygous variant carriers

477

954

1430

1907

2384

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

246

492

738

984

1230

<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:

0.00383

AC:

583

AN:

152382

Hom.:

Cov.:

AF XY:

0.00358

AC XY:

267

AN XY:

74518

show subpopulations

African (AFR)

AF:

0.00101

AC:

AN:

41594

American (AMR)

AF:

0.00496

AC:

AN:

15310

Ashkenazi Jewish (ASJ)

AF:

0.00374

AC:

AN:

3472

East Asian (EAS)

AF:

0.00

AC:

AN:

5186

South Asian (SAS)

AF:

0.00476

AC:

AN:

4834

European-Finnish (FIN)

AF:

0.000753

AC:

AN:

10628

Middle Eastern (MID)

AF:

0.0136

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.00594

AC:

404

AN:

68038

Other (OTH)

AF:

0.00615

AC:

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.498

Heterozygous variant carriers

126

157

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

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:

0.00489

Hom.:

Bravo

AF:

0.00435

TwinsUK

AF:

0.00485

AC:

ALSPAC

AF:

0.00441

AC:

ESP6500AA

AF:

0.000716

AC:

ESP6500EA

AF:

0.00652

AC:

ExAC

AF:

0.00485

AC:

582

Asia WGS

AF:

0.00202

AC:

AN:

3478

ClinVar

ClinVar submissions

Significance:Conflicting classifications of pathogenicity

Revision:criteria provided, conflicting classifications

View on ClinVar

Pathogenic

VUS

Benign

Condition

not provided (6)

not specified (3)

Baller-Gerold syndrome (1)

Hereditary cancer-predisposing syndrome (1)

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.14

BayesDel_addAF

Benign

-0.29

BayesDel_noAF

Benign

-0.19

CADD

Benign

(source)

DANN

Benign

0.75

DEOGEN2

Benign

0.0070

FATHMM_MKL

Benign

0.36

LIST_S2

Benign

0.70

MetaRNN

Benign

0.0039

MutationAssessor

Benign

0.34

PhyloP100

0.18

PrimateAI

Benign

0.36

Sift4G

Benign

0.55

Polyphen

0.024

Vest4

0.32

MVP

0.72

GERP RS

3.5

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.0

Varity_R

0.16

gMVP

0.45

Mutation Taster

=94/6

polymorphism

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

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

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over