rs1876482

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The variant allele was found at a frequency of 0.0905 in 152,244 control chromosomes in the GnomAD database, including 2,115 homozygotes. 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: 𝑓 0.091 ( 2115 hom., cov: 32)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.141
Variant links:

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ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.89).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.734 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt

Frequencies

GnomAD3 genomes
AF:
0.0905
AC:
13768
AN:
152126
Hom.:
2110
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0168
Gnomad AMI
AF:
0.119
Gnomad AMR
AF:
0.159
Gnomad ASJ
AF:
0.0323
Gnomad EAS
AF:
0.753
Gnomad SAS
AF:
0.209
Gnomad FIN
AF:
0.135
Gnomad MID
AF:
0.0316
Gnomad NFE
AF:
0.0564
Gnomad OTH
AF:
0.112
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.0905
AC:
13785
AN:
152244
Hom.:
2115
Cov.:
32
AF XY:
0.100
AC XY:
7472
AN XY:
74440
show subpopulations
Gnomad4 AFR
AF:
0.0167
Gnomad4 AMR
AF:
0.159
Gnomad4 ASJ
AF:
0.0323
Gnomad4 EAS
AF:
0.753
Gnomad4 SAS
AF:
0.209
Gnomad4 FIN
AF:
0.135
Gnomad4 NFE
AF:
0.0565
Gnomad4 OTH
AF:
0.119
Alfa
AF:
0.0625
Hom.:
114
Bravo
AF:
0.0934
Asia WGS
AF:
0.456
AC:
1581
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.89
CADD
Benign
2.9
DANN
Benign
0.30

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: rs1876482; hg19: chr2-17362568; API