Variant 17-75630842-G-GTGT details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBA1

The NM_004259.7(RECQL5):c.1586-6_1586-5insACA variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0631 in 1,139,402 control chromosomes in the GnomAD database, including 1,959 homozygotes. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.059 ( 269 hom., cov: 21)

Exomes 𝑓: 0.063 ( 1959 hom. )

Failed GnomAD Quality Control

Consequence

RECQL5
NM_004259.7 splice_region, intron

Scores

Not classified

Clinical Significance

Benign criteria provided, single submitter B:2

Conservation

PhyloP100: 0.258

Variant links:

Genes affected

RECQL5 (HGNC:9950): (RecQ like helicase 5) The protein encoded by this gene is a helicase that is important for genome stability. The encoded protein also prevents aberrant homologous recombination by displacing RAD51 from ssDNA. Three transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2011]

RECQL5 links:

RECQL5 (HGNC:):

RECQL5 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP6

Variant 17-75630842-G-GTGT is Benign according to our data. Variant chr17-75630842-G-GTGT is described in ClinVar as [Benign]. Clinvar id is 403370.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAdExome4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0689 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
RECQL5	NM_004259.7 linkuse as main transcript	c.1586-6_1586-5insACA		splice_region_variant, intron_variant		ENST00000317905.10	NP_004250.4	O94762-1A0A024R8M9Q8WYH5

Ensembl

Gene	Transcript	HGVSc	Effect	TSL	MANE	Protein	UniProt
RECQL5	ENST00000317905.10 linkuse as main transcript	c.1586-6_1586-5insACA	splice_region_variant, intron_variant	1	NM_004259.7	ENSP00000317636.5	O94762-1
RECQL5	ENST00000423245.6 linkuse as main transcript	c.1505-6_1505-5insACA	splice_region_variant, intron_variant	1		ENSP00000394820.2	O94762-4
RECQL5	ENST00000443199.6 linkuse as main transcript	n.1122-6_1122-5insACA	splice_region_variant, intron_variant	1
RECQL5	ENST00000580707.1 linkuse as main transcript	c.53-6_53-5insACA	splice_region_variant, intron_variant	3		ENSP00000463701.1	J3QLU0

Frequencies

GnomAD3 genomes

AF:

0.00

AC:

6424

AN:

108212

Hom.:

269

Cov.:

FAILED QC

Gnomad AFR

AF:

0.0203

Gnomad AMI

AF:

0.130

Gnomad AMR

AF:

0.0391

Gnomad ASJ

AF:

0.0435

Gnomad EAS

AF:

0.00480

Gnomad SAS

AF:

0.0338

Gnomad FIN

AF:

0.0622

Gnomad MID

AF:

0.0690

Gnomad NFE

AF:

0.0835

Gnomad OTH

AF:

0.0531

GnomAD3 exomes

AF:

0.124

AC:

7134

AN:

57474

Hom.:

1182

AF XY:

0.122

AC XY:

3536

AN XY:

28946

show subpopulations

Gnomad AFR exome

AF:

0.0323

Gnomad AMR exome

AF:

0.0790

Gnomad ASJ exome

AF:

0.106

Gnomad EAS exome

AF:

0.0570

Gnomad SAS exome

AF:

0.104

Gnomad FIN exome

AF:

0.194

Gnomad NFE exome

AF:

0.171

Gnomad OTH exome

AF:

0.124

GnomAD4 exome

AF:

0.0631

AC:

71928

AN:

1139402

Hom.:

1959

Cov.:

AF XY:

0.0628

AC XY:

35040

AN XY:

557830

show subpopulations

Gnomad4 AFR exome

AF:

0.0135

Gnomad4 AMR exome

AF:

0.0320

Gnomad4 ASJ exome

AF:

0.0395

Gnomad4 EAS exome

AF:

0.00380

Gnomad4 SAS exome

AF:

0.0370

Gnomad4 FIN exome

AF:

0.0668

Gnomad4 NFE exome

AF:

0.0694

Gnomad4 OTH exome

AF:

0.0543

GnomAD4 genome

Data not reliable, filtered out with message: AS_VQSR

AF:

0.0593

AC:

6423

AN:

108248

Hom.:

269

Cov.:

AF XY:

0.0560

AC XY:

2916

AN XY:

52056

show subpopulations

Gnomad4 AFR

AF:

0.0202

Gnomad4 AMR

AF:

0.0390

Gnomad4 ASJ

AF:

0.0435

Gnomad4 EAS

AF:

0.00456

Gnomad4 SAS

AF:

0.0338

Gnomad4 FIN

AF:

0.0622

Gnomad4 NFE

AF:

0.0835

Gnomad4 OTH

AF:

0.0530

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not specified

Benign:1

Benign, criteria provided, single submitter

clinical testing

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

Mar 29, 2016

Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or databases. Disclaimer: This variant has not undergone full assessment. The following are preliminary notes: Frequency -

RECQL5-related disorder

Benign:1

Benign, no assertion criteria provided

clinical testing

PreventionGenetics, part of Exact Sciences

Nov 04, 2019

This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

Splicing

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