Genetic Variant RECQL5:c.1586-6_1586-5insA (chr17-75630842-G-GT) – ACMG Classification: Benign (-9 pts)

Variant summary

Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP6BA1

The NM_004259.7(RECQL5):c.1586-6_1586-5insA variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.591 in 1,254,226 control chromosomes in the GnomAD database, including 196,727 homozygotes. 1/1 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Benign (no stars).

Frequency

Genomes: 𝑓 0.60 ( 16451 hom., cov: 21)

Exomes 𝑓: 0.59 ( 180276 hom. )

Consequence

RECQL5
NM_004259.7 splice_region, intron

Scores

Not classified

Clinical Significance

Benign no assertion criteria provided B:1

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:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -9 ACMG points.

BP6

Variant 17-75630842-G-GT is Benign according to our data. Variant chr17-75630842-G-GT is described in ClinVar as [Benign]. Clinvar id is 3059523.Status of the report is no_assertion_criteria_provided, 0 stars.

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.611 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
RECQL5	NM_004259.7 link	c.1586-6_1586-5insA		splice_region_variant, intron_variant	Intron 11 of 19	ENST00000317905.10	NP_004250.4	O94762-1A0A024R8M9Q8WYH5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
RECQL5	ENST00000317905.10 link	c.1586-6_1586-5insA		splice_region_variant, intron_variant	Intron 11 of 19	1	NM_004259.7	ENSP00000317636.5		O94762-1
RECQL5	ENST00000423245.6 link	c.1505-6_1505-5insA		splice_region_variant, intron_variant	Intron 11 of 19	1		ENSP00000394820.2		O94762-4

Frequencies

GnomAD3 genomes

AF:

0.598

AC:

64768

AN:

108364

Hom.:

16444

Cov.:

show subpopulations

Gnomad AFR

AF:

0.536

Gnomad AMI

AF:

0.598

Gnomad AMR

AF:

0.586

Gnomad ASJ

AF:

0.561

Gnomad EAS

AF:

0.586

Gnomad SAS

AF:

0.632

Gnomad FIN

AF:

0.654

Gnomad MID

AF:

0.616

Gnomad NFE

AF:

0.617

Gnomad OTH

AF:

0.594

GnomAD3 exomes

AF:

0.387

AC:

22223

AN:

57474

Hom.:

3187

AF XY:

0.390

AC XY:

11280

AN XY:

28946

show subpopulations

Gnomad AFR exome

AF:

0.424

Gnomad AMR exome

AF:

0.332

Gnomad ASJ exome

AF:

0.330

Gnomad EAS exome

AF:

0.391

Gnomad SAS exome

AF:

0.383

Gnomad FIN exome

AF:

0.381

Gnomad NFE exome

AF:

0.408

Gnomad OTH exome

AF:

0.398

GnomAD4 exome

AF:

0.591

AC:

676972

AN:

1145826

Hom.:

180276

Cov.:

AF XY:

0.591

AC XY:

331816

AN XY:

561020

show subpopulations

Gnomad4 AFR exome

AF:

0.400

Gnomad4 AMR exome

AF:

0.603

Gnomad4 ASJ exome

AF:

0.536

Gnomad4 EAS exome

AF:

0.624

Gnomad4 SAS exome

AF:

0.592

Gnomad4 FIN exome

AF:

0.621

Gnomad4 NFE exome

AF:

0.595

Gnomad4 OTH exome

AF:

0.582

GnomAD4 genome

AF:

0.598

AC:

64791

AN:

108400

Hom.:

16451

Cov.:

AF XY:

0.603

AC XY:

31431

AN XY:

52154

show subpopulations

Gnomad4 AFR

AF:

0.536

Gnomad4 AMR

AF:

0.585

Gnomad4 ASJ

AF:

0.561

Gnomad4 EAS

AF:

0.586

Gnomad4 SAS

AF:

0.633

Gnomad4 FIN

AF:

0.654

Gnomad4 NFE

AF:

0.617

Gnomad4 OTH

AF:

0.597

Bravo

AF:

0.0405

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: no assertion criteria provided

LINK: link

Submissions by phenotype

RECQL5-related disorder

Benign:1

Nov 04, 2019

PreventionGenetics, part of Exact Sciences

Significance: Benign

Review Status: no assertion criteria provided

Collection Method: clinical testing

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

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.030

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