rs918980

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 0.482 in 152,000 control chromosomes in the GnomAD database, including 17,895 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 0.48 ( 17895 hom., cov: 32)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.35
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=-0.96).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.543 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt

Frequencies

GnomAD3 genomes
AF:
0.482
AC:
73176
AN:
151882
Hom.:
17890
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.549
Gnomad AMI
AF:
0.520
Gnomad AMR
AF:
0.459
Gnomad ASJ
AF:
0.467
Gnomad EAS
AF:
0.364
Gnomad SAS
AF:
0.380
Gnomad FIN
AF:
0.501
Gnomad MID
AF:
0.481
Gnomad NFE
AF:
0.459
Gnomad OTH
AF:
0.487
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.482
AC:
73222
AN:
152000
Hom.:
17895
Cov.:
32
AF XY:
0.482
AC XY:
35819
AN XY:
74300
show subpopulations
Gnomad4 AFR
AF:
0.549
Gnomad4 AMR
AF:
0.459
Gnomad4 ASJ
AF:
0.467
Gnomad4 EAS
AF:
0.363
Gnomad4 SAS
AF:
0.380
Gnomad4 FIN
AF:
0.501
Gnomad4 NFE
AF:
0.459
Gnomad4 OTH
AF:
0.484
Alfa
AF:
0.456
Hom.:
7171
Bravo
AF:
0.483
Asia WGS
AF:
0.380
AC:
1320
AN:
3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.96
CADD
Benign
3.9
DANN
Benign
0.34

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: rs918980; hg19: chr7-37601898; API