rs10986795
Variant names:
Your query was ambiguous. Multiple possible variants found:
Variant summary
Our verdict is Uncertain significance. The variant received 2 ACMG points: 2P and 0B. PM2
The NM_020207.7(ERCC6L2):c.-32T>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 0.000000704 in 1,421,120 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: not found (cov: 33)
Exomes 𝑓: 7.0e-7 ( 0 hom. )
Consequence
ERCC6L2
NM_020207.7 5_prime_UTR
NM_020207.7 5_prime_UTR
Scores
2
3
9
Clinical Significance
Conservation
PhyloP100: -0.603
Publications
3 publications found
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]
Genome browser will be placed here
ACMG classification
Classification was made for transcript
Our verdict: Uncertain_significance. The variant received 2 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
Variant Effect in Transcripts
ACMG analysis was done for transcript: NM_020207.7. You can select a different transcript below to see updated ACMG assignments.
RefSeq Transcripts
Ensembl Transcripts
| Sel. | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| ERCC6L2 | MANE Select | c.-32T>G | 5_prime_UTR | Exon 1 of 19 | ENSP00000499221.2 | Q5T890-1 | |||
| ERCC6L2 | TSL:1 | c.-32T>G | 5_prime_UTR | Exon 1 of 14 | ENSP00000288985.8 | A0A5F9UKL4 | |||
| ERCC6L2-AS1 | TSL:1 | n.4A>C | non_coding_transcript_exon | Exon 1 of 3 |
Frequencies
GnomAD3 genomes
GnomAD3 genomes
Cov.:
33
GnomAD2 exomes AF: 0.00 AC: 0AN: 184594 AF XY: 0.00
GnomAD2 exomes
AF:
AC:
0
AN:
184594
AF XY:
Gnomad AFR exome
AF:
Gnomad AMR exome
AF:
Gnomad ASJ exome
AF:
Gnomad EAS exome
AF:
Gnomad FIN exome
AF:
Gnomad NFE exome
AF:
Gnomad OTH exome
AF:
GnomAD4 exome AF: 7.04e-7 AC: 1AN: 1421120Hom.: 0 Cov.: 31 AF XY: 0.00000142 AC XY: 1AN XY: 703290 show subpopulations
GnomAD4 exome
AF:
AC:
1
AN:
1421120
Hom.:
Cov.:
31
AF XY:
AC XY:
1
AN XY:
703290
show subpopulations
African (AFR)
AF:
AC:
0
AN:
32332
American (AMR)
AF:
AC:
0
AN:
39752
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
25364
East Asian (EAS)
AF:
AC:
1
AN:
36930
South Asian (SAS)
AF:
AC:
0
AN:
80936
European-Finnish (FIN)
AF:
AC:
0
AN:
48682
Middle Eastern (MID)
AF:
AC:
0
AN:
5722
European-Non Finnish (NFE)
AF:
AC:
0
AN:
1092590
Other (OTH)
AF:
AC:
0
AN:
58812
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.475
Heterozygous variant carriers
0
0
1
1
2
2
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
GnomAD4 genome
GnomAD4 genome
Cov.:
33
ClinVar
ClinVar submissions
View on ClinVar Significance:Uncertain significance
Revision:criteria provided, single submitter
Pathogenic
VUS
Benign
Condition
-
1
-
not provided (1)
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_addAF
Pathogenic
D
BayesDel_noAF
Benign
DANN
Benign
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Benign
N
LIST_S2
Uncertain
D
M_CAP
Benign
D
MetaRNN
Uncertain
D
MetaSVM
Benign
T
PhyloP100
PROVEAN
Benign
N
REVEL
Benign
Sift
Uncertain
D
Sift4G
Pathogenic
D
Vest4
MutPred
Gain of methylation at M1 (P = 0.0322)
MVP
ClinPred
T
GERP RS
gMVP
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.