rs959186

chr6-88484275-G-A

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;