Menu
GeneBe

rs660895

chr6-32609603-A-G

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 0.195 in 152042 control chromosomes in the gnomAD Genomes database, including 3133 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 0.20 ( 3133 hom., cov: 31)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.386

Links

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.88).
BA1
?
GnomAd highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.283 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:
0.195
AC:
29656
AN:
152042
Hom.:
3133
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.146
Gnomad AMI
AF:
0.204
Gnomad AMR
AF:
0.290
Gnomad ASJ
AF:
0.211
Gnomad EAS
AF:
0.267
Gnomad SAS
AF:
0.128
Gnomad FIN
AF:
0.254
Gnomad MID
AF:
0.161
Gnomad NFE
AF:
0.194
Gnomad OTH
AF:
0.172
Alfa
AF:
0.194
Hom.:
4728
Bravo
AF:
0.202
Asia WGS
AF:
0.224
AC:
780
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
7.7
Dann
Benign
0.52

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: rs660895; hg19: chr6-32577380;