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GeneBe

rs11615

Variant summary

Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1

The NM_001983(ERCC1):c.354T>C(p.Asn118=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.552 in 151840 control chromosomes in the gnomAD Genomes database, including 26919 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (β˜…β˜…).

Frequency

Genomes: 𝑓 0.55 ( 26919 hom., cov: 31)
Exomes 𝑓: 0.50 ( 35330 hom. )

Consequence

ERCC1
NM_001983 synonymous

Scores

2

Clinical Significance

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

Conservation

PhyloP100: -0.629

Links

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -21 ACMG points.

BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.83).
BP6
?
Variant 19:45420395-A>G is Benign according to our data. Variant chr19-45420395-A-G is described in ClinVar as [Benign]. Clinvar id is 225945. Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr19-45420395-A-G is described in Lovd as [Benign].
BP7
?
Synonymous conserved (PhyloP=-0.629 with no splicing effect.
BA1
?
GnomAd highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.867 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
ERCC1NM_001983.4 linkuse as main transcriptc.354T>C p.Asn118= synonymous_variant 4/10 ENST00000300853.8

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
ERCC1ENST00000300853.8 linkuse as main transcriptc.354T>C p.Asn118= synonymous_variant 4/101 NM_001983.4 P1P07992-1

Frequencies

GnomAD3 genomes
AF:
0.552
AC:
83875
AN:
151840
Hom.:
26919
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.875
Gnomad AMI
AF:
0.478
Gnomad AMR
AF:
0.596
Gnomad ASJ
AF:
0.396
Gnomad EAS
AF:
0.737
Gnomad SAS
AF:
0.544
Gnomad FIN
AF:
0.362
Gnomad MID
AF:
0.436
Gnomad NFE
AF:
0.373
Gnomad OTH
AF:
0.518
GnomAD3 exomes
AF:
0.501
AC:
125107
AN:
249686
Hom.:
35330
AF XY:
0.485
AC XY:
65375
AN XY:
134914
show subpopulations
Gnomad AFR exome
AF:
0.890
Gnomad AMR exome
AF:
0.705
Gnomad ASJ exome
AF:
0.415
Gnomad EAS exome
AF:
0.734
Gnomad SAS exome
AF:
0.529
Gnomad FIN exome
AF:
0.363
Gnomad NFE exome
AF:
0.374
Gnomad OTH exome
AF:
0.448
GnomAD4 exome
AF:
0.415
AC:
606069
AN:
1459736
Hom.:
136082
AF XY:
0.416
AC XY:
301953
AN XY:
726166
show subpopulations
Gnomad4 AFR exome
AF:
0.893
Gnomad4 AMR exome
AF:
0.689
Gnomad4 ASJ exome
AF:
0.405
Gnomad4 EAS exome
AF:
0.727
Gnomad4 SAS exome
AF:
0.528
Gnomad4 FIN exome
AF:
0.366
Gnomad4 NFE exome
AF:
0.370
Gnomad4 OTH exome
AF:
0.452
Alfa
AF:
0.414
Hom.:
34822
Bravo
AF:
0.584
Asia WGS
AF:
0.667
AC:
2322
AN:
3478
EpiCase
AF:
0.381
EpiControl
AF:
0.384

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 submitterclinical testingGeneDxNov 10, 2018- -
Benign, criteria provided, single submitterclinical testingInvitaeNov 01, 2022- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.83
Cadd
Benign
0.23
Dann
Benign
0.42
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.7

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.

Other links and lift over

dbSNP: rs11615; hg19: chr19-45923653;