Variant rs10512243 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_020207.7(ERCC6L2):c.4627G>A(p.Ala1543Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0911 in 1,364,476 control chromosomes in the GnomAD database, including 6,279 homozygotes. In-silico tool predicts a benign outcome for this variant. 4/4 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.088 ( 668 hom., cov: 33)

Exomes 𝑓: 0.092 ( 5611 hom. )

Consequence

ERCC6L2
NM_020207.7 missense

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: 0.125

Variant links:

Genes affected

ERCC6L2 (HGNC:26922): (ERCC excision repair 6 like 2) This gene encodes a member of the Snf2 family of helicase-like proteins. The encoded protein may play a role in DNA repair and mitochondrial function. Mutations in this gene have been associated with bone marrow failure syndrome 2. Alternatively spliced transcript variants that encode different protein isoforms have been described. [provided by RefSeq, Apr 2014]

ERCC6L2 links:

ERCC6L2 (HGNC:):

ERCC6L2 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

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

BP6

Variant 9-96013177-G-A is Benign according to our data. Variant chr9-96013177-G-A is described in ClinVar as [Benign]. Clinvar id is 1167166.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.13 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ERCC6L2	NM_020207.7 linkuse as main transcript	c.4627G>A	p.Ala1543Thr	missense_variant	19/19	ENST00000653738.2	NP_064592.3	Q5T890

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ERCC6L2	ENST00000653738.2 linkuse as main transcript	c.4627G>A	p.Ala1543Thr	missense_variant	19/19		NM_020207.7	ENSP00000499221.2		A0A590UJ07

Frequencies

GnomAD3 genomes

AF:

0.0879

AC:

13361

AN:

152030

Hom.:

666

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0686

Gnomad AMI

AF:

0.0230

Gnomad AMR

AF:

0.135

Gnomad ASJ

AF:

0.0585

Gnomad EAS

AF:

0.0519

Gnomad SAS

AF:

0.0884

Gnomad FIN

AF:

0.122

Gnomad MID

AF:

0.0380

Gnomad NFE

AF:

0.0891

Gnomad OTH

AF:

0.0906

GnomAD3 exomes

AF:

0.104

AC:

25457

AN:

245288

Hom.:

1613

AF XY:

0.0992

AC XY:

13212

AN XY:

133180

show subpopulations

Gnomad AFR exome

AF:

0.0697

Gnomad AMR exome

AF:

0.198

Gnomad ASJ exome

AF:

0.0602

Gnomad EAS exome

AF:

0.0565

Gnomad SAS exome

AF:

0.0898

Gnomad FIN exome

AF:

0.123

Gnomad NFE exome

AF:

0.0917

Gnomad OTH exome

AF:

0.101

GnomAD4 exome

AF:

0.0915

AC:

110964

AN:

1212328

Hom.:

5611

Cov.:

AF XY:

0.0909

AC XY:

54637

AN XY:

601066

show subpopulations

Gnomad4 AFR exome

AF:

0.0643

Gnomad4 AMR exome

AF:

0.197

Gnomad4 ASJ exome

AF:

0.0607

Gnomad4 EAS exome

AF:

0.0583

Gnomad4 SAS exome

AF:

0.0886

Gnomad4 FIN exome

AF:

0.124

Gnomad4 NFE exome

AF:

0.0893

Gnomad4 OTH exome

AF:

0.0804

GnomAD4 genome

AF:

0.0879

AC:

13374

AN:

152148

Hom.:

668

Cov.:

AF XY:

0.0899

AC XY:

6689

AN XY:

74364

show subpopulations

Gnomad4 AFR

AF:

0.0685

Gnomad4 AMR

AF:

0.135

Gnomad4 ASJ

AF:

0.0585

Gnomad4 EAS

AF:

0.0519

Gnomad4 SAS

AF:

0.0885

Gnomad4 FIN

AF:

0.122

Gnomad4 NFE

AF:

0.0890

Gnomad4 OTH

AF:

0.0906

Alfa

AF:

0.0861

Hom.:

966

Bravo

AF:

0.0892

Asia WGS

AF:

0.0720

AC:

249

AN:

3478

EpiCase

AF:

0.0825

EpiControl

AF:

0.0856

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Feb 01, 2024	- -
Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.85

CADD

Benign

0.26

DANN

Benign

0.18

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