rs959186

Variant names:

• chr6-88484275-G-A
• rs959186

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.107 in 152,074 control chromosomes in the GnomAD database, including 940 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 0.11 (940 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.414

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.128 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: 0.107 AC: 16236 AN: 151956 Hom.: 941 Cov.: 32

Gnomad AFR AF: 0.0833

Gnomad AMI AF: 0.124

Gnomad AMR AF: 0.102

Gnomad ASJ AF: 0.158

Gnomad EAS AF: 0.0358

Gnomad SAS AF: 0.0499

Gnomad FIN AF: 0.0851

Gnomad MID AF: 0.180

Gnomad NFE AF: 0.131

Gnomad OTH AF: 0.139

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.107 AC: 16235 AN: 152074 Hom.: 940 Cov.: 32 AF XY: 0.104 AC XY: 7714 AN XY: 74332

Gnomad4 AFR AF: 0.0833

Gnomad4 AMR AF: 0.102

Gnomad4 ASJ AF: 0.158

Gnomad4 EAS AF: 0.0359

Gnomad4 SAS AF: 0.0502

Gnomad4 FIN AF: 0.0851

Gnomad4 NFE AF: 0.131

Gnomad4 OTH AF: 0.137

Alfa AF: 0.126 Hom.: 778

Bravo AF: 0.109

Asia WGS AF: 0.0430 AC: 150 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.3
DANN	Benign	0.64

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs959186; hg19: chr6-89193994;