rs9347131

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 0.135 in 152,234 control chromosomes in the GnomAD database, including 1,963 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 0.13 ( 1963 hom., cov: 32)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -4.78
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=-0.9).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.398 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:
0.134
AC:
20430
AN:
152116
Hom.:
1949
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.131
Gnomad AMI
AF:
0.0691
Gnomad AMR
AF:
0.293
Gnomad ASJ
AF:
0.0487
Gnomad EAS
AF:
0.413
Gnomad SAS
AF:
0.154
Gnomad FIN
AF:
0.0977
Gnomad MID
AF:
0.0828
Gnomad NFE
AF:
0.0894
Gnomad OTH
AF:
0.128
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.135
AC:
20485
AN:
152234
Hom.:
1963
Cov.:
32
AF XY:
0.139
AC XY:
10351
AN XY:
74440
show subpopulations
Gnomad4 AFR
AF:
0.132
Gnomad4 AMR
AF:
0.294
Gnomad4 ASJ
AF:
0.0487
Gnomad4 EAS
AF:
0.412
Gnomad4 SAS
AF:
0.155
Gnomad4 FIN
AF:
0.0977
Gnomad4 NFE
AF:
0.0894
Gnomad4 OTH
AF:
0.131
Alfa
AF:
0.0997
Hom.:
1591
Bravo
AF:
0.152
Asia WGS
AF:
0.260
AC:
904
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.90
CADD
Benign
0.14
DANN
Benign
0.39

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: rs9347131; hg19: chr6-158634878; API