rs56108623

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate

The NM_020207.7(ERCC6L2):​c.-15C>G variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000698 in 1,432,190 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: not found (cov: 32)
Exomes 𝑓: 7.0e-7 ( 0 hom. )

Consequence

ERCC6L2
NM_020207.7 5_prime_UTR

Scores

2
3
11

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.20
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-AS1 (HGNC:27858): (ERCC6L2 antisense RNA 1)

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 0 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.086993754).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
ERCC6L2NM_020207.7 linkc.-15C>G 5_prime_UTR_variant Exon 1 of 19 ENST00000653738.2 NP_064592.3 Q5T890

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
ERCC6L2ENST00000653738 linkc.-15C>G 5_prime_UTR_variant Exon 1 of 19 NM_020207.7 ENSP00000499221.2 A0A590UJ07

Frequencies

GnomAD3 genomes
Cov.:
32
GnomAD3 exomes
AF:
0.00000501
AC:
1
AN:
199718
Hom.:
0
AF XY:
0.00
AC XY:
0
AN XY:
108922
show subpopulations
Gnomad AFR exome
AF:
0.00
Gnomad AMR exome
AF:
0.00
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.0000679
Gnomad SAS exome
AF:
0.00
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.00
Gnomad OTH exome
AF:
0.00
GnomAD4 exome
AF:
6.98e-7
AC:
1
AN:
1432190
Hom.:
0
Cov.:
32
AF XY:
0.00
AC XY:
0
AN XY:
709980
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.0000266
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.00
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
Cov.:
32
Bravo
AF:
0.00000378

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_addAF
Benign
-0.023
T
BayesDel_noAF
Uncertain
-0.080
CADD
Benign
19
DANN
Uncertain
0.99
Eigen
Benign
-0.70
Eigen_PC
Benign
-0.72
FATHMM_MKL
Benign
0.0080
N
LIST_S2
Benign
0.43
T
M_CAP
Benign
0.033
D
MetaRNN
Benign
0.087
T
MetaSVM
Uncertain
-0.20
T
PrimateAI
Benign
0.42
T
PROVEAN
Benign
-0.35
N
REVEL
Benign
0.14
Sift
Pathogenic
0.0
D
Sift4G
Pathogenic
0.0
D
Vest4
0.23
MutPred
0.12
Loss of glycosylation at P8 (P = 0.0538);
MVP
0.47
MPC
0.21
ClinPred
0.51
D
GERP RS
3.2
gMVP
0.11

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

LitVar

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

Other links and lift over

dbSNP: rs56108623; hg19: chr9-98638306; API