rs9261394

Variant names:

• chr6-30096785-A-G
• rs9261394

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 0.631 in 152,034 control chromosomes in the GnomAD database, including 30,743 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 0.63 (30743 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.62

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.743 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: 0.630 AC: 95756 AN: 151914 Hom.: 30694 Cov.: 31

Gnomad AFR AF: 0.750

Gnomad AMI AF: 0.647

Gnomad AMR AF: 0.611

Gnomad ASJ AF: 0.651

Gnomad EAS AF: 0.592

Gnomad SAS AF: 0.620

Gnomad FIN AF: 0.526

Gnomad MID AF: 0.652

Gnomad NFE AF: 0.580

Gnomad OTH AF: 0.643

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

GnomAD4 genome AF: 0.631 AC: 95858 AN: 152034 Hom.: 30743 Cov.: 31 AF XY: 0.627 AC XY: 46610 AN XY: 74302

Gnomad4 AFR AF: 0.750

Gnomad4 AMR AF: 0.611

Gnomad4 ASJ AF: 0.651

Gnomad4 EAS AF: 0.592

Gnomad4 SAS AF: 0.621

Gnomad4 FIN AF: 0.526

Gnomad4 NFE AF: 0.580

Gnomad4 OTH AF: 0.646

Alfa AF: 0.592 Hom.: 16929

Bravo AF: 0.646

Asia WGS AF: 0.609 AC: 2118 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.12
DANN	Benign	0.47

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9261394; hg19: chr6-30064562;