rs9267463

Variant names:

• chr6-31522703-G-A
• rs9267463

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.0558 in 152,066 control chromosomes in the GnomAD database, including 270 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 0.056 (270 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.223
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0602 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: 0.0557 AC: 8467 AN: 151948 Hom.: 267 Cov.: 32

Gnomad AFR AF: 0.0540

Gnomad AMI AF: 0.157

Gnomad AMR AF: 0.0561

Gnomad ASJ AF: 0.0813

Gnomad EAS AF: 0.0264

Gnomad SAS AF: 0.0626

Gnomad FIN AF: 0.0145

Gnomad MID AF: 0.0443

Gnomad NFE AF: 0.0617

Gnomad OTH AF: 0.0722

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

GnomAD4 genome AF: 0.0558 AC: 8488 AN: 152066 Hom.: 270 Cov.: 32 AF XY: 0.0542 AC XY: 4031 AN XY: 74332

African (AFR) AF: 0.0545 AC: 2257 AN: 41450

American (AMR) AF: 0.0561 AC: 857 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.0813 AC: 282 AN: 3468

East Asian (EAS) AF: 0.0264 AC: 137 AN: 5180

South Asian (SAS) AF: 0.0619 AC: 298 AN: 4818

European-Finnish (FIN) AF: 0.0145 AC: 153 AN: 10570

Middle Eastern (MID) AF: 0.0476 AC: 14 AN: 294

European-Non Finnish (NFE) AF: 0.0617 AC: 4196 AN: 67994

Other (OTH) AF: 0.0715 AC: 151 AN: 2112

Alfa AF: 0.0548 Hom.: 40

Bravo AF: 0.0581

Asia WGS AF: 0.0430 AC: 148 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.5
DANN	Benign	0.75
PhyloP100		-0.22

Splicing

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

Other links and lift over

dbSNP: rs9267463; hg19: chr6-31490480;