rs9267649

Variant names:

• chr6-31857051-A-G
• rs9267649

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 0.878 in 152,110 control chromosomes in the GnomAD database, including 58,882 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 0.88 (58882 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.11

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.958 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: 0.877 AC: 133360 AN: 151992 Hom.: 58818 Cov.: 31

Gnomad AFR AF: 0.966

Gnomad AMI AF: 0.774

Gnomad AMR AF: 0.914

Gnomad ASJ AF: 0.934

Gnomad EAS AF: 0.804

Gnomad SAS AF: 0.882

Gnomad FIN AF: 0.844

Gnomad MID AF: 0.943

Gnomad NFE AF: 0.823

Gnomad OTH AF: 0.905

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

GnomAD4 genome AF: 0.878 AC: 133484 AN: 152110 Hom.: 58882 Cov.: 31 AF XY: 0.878 AC XY: 65264 AN XY: 74366

Gnomad4 AFR AF: 0.966

Gnomad4 AMR AF: 0.914

Gnomad4 ASJ AF: 0.934

Gnomad4 EAS AF: 0.804

Gnomad4 SAS AF: 0.882

Gnomad4 FIN AF: 0.844

Gnomad4 NFE AF: 0.823

Gnomad4 OTH AF: 0.905

Alfa AF: 0.838 Hom.: 82066

Bravo AF: 0.887

Asia WGS AF: 0.895 AC: 3116 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.16
DANN	Benign	0.36

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9267649; hg19: chr6-31824828;