rs7176005

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 0.211 in 152,140 control chromosomes in the GnomAD database, including 4,793 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 0.21 ( 4793 hom., cov: 32)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.634
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=-0.88).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.415 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:
0.211
AC:
32071
AN:
152020
Hom.:
4777
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.420
Gnomad AMI
AF:
0.110
Gnomad AMR
AF:
0.173
Gnomad ASJ
AF:
0.139
Gnomad EAS
AF:
0.208
Gnomad SAS
AF:
0.260
Gnomad FIN
AF:
0.0637
Gnomad MID
AF:
0.180
Gnomad NFE
AF:
0.118
Gnomad OTH
AF:
0.198
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.211
AC:
32141
AN:
152140
Hom.:
4793
Cov.:
32
AF XY:
0.211
AC XY:
15663
AN XY:
74378
show subpopulations
Gnomad4 AFR
AF:
0.420
Gnomad4 AMR
AF:
0.173
Gnomad4 ASJ
AF:
0.139
Gnomad4 EAS
AF:
0.208
Gnomad4 SAS
AF:
0.259
Gnomad4 FIN
AF:
0.0637
Gnomad4 NFE
AF:
0.118
Gnomad4 OTH
AF:
0.202
Alfa
AF:
0.147
Hom.:
554
Bravo
AF:
0.227
Asia WGS
AF:
0.290
AC:
1009
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.88
CADD
Benign
7.2
DANN
Benign
0.46

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: rs7176005; hg19: chr15-51631279; API