rs9501587

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 0.288 in 152,000 control chromosomes in the GnomAD database, including 7,297 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 0.29 ( 7297 hom., cov: 31)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.146
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=-0.72).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.446 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt

Ensembl

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

Frequencies

GnomAD3 genomes
AF:
0.288
AC:
43735
AN:
151884
Hom.:
7290
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.451
Gnomad AMI
AF:
0.356
Gnomad AMR
AF:
0.342
Gnomad ASJ
AF:
0.278
Gnomad EAS
AF:
0.143
Gnomad SAS
AF:
0.323
Gnomad FIN
AF:
0.180
Gnomad MID
AF:
0.376
Gnomad NFE
AF:
0.200
Gnomad OTH
AF:
0.335
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.288
AC:
43786
AN:
152000
Hom.:
7297
Cov.:
31
AF XY:
0.289
AC XY:
21447
AN XY:
74306
show subpopulations
Gnomad4 AFR
AF:
0.451
Gnomad4 AMR
AF:
0.342
Gnomad4 ASJ
AF:
0.278
Gnomad4 EAS
AF:
0.144
Gnomad4 SAS
AF:
0.322
Gnomad4 FIN
AF:
0.180
Gnomad4 NFE
AF:
0.200
Gnomad4 OTH
AF:
0.331
Alfa
AF:
0.206
Hom.:
3069
Bravo
AF:
0.308
Asia WGS
AF:
0.239
AC:
830
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.72
CADD
Benign
10
DANN
Benign
0.89

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: rs9501587; hg19: chr6-31346937; API