rs9276490

Variant names:

• chr6-32750904-A-G
• rs9276490

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 0.617 in 151,950 control chromosomes in the GnomAD database, including 29,338 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 0.62 (29338 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.637

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.794 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: 0.617 AC: 93626 AN: 151830 Hom.: 29301 Cov.: 32

Gnomad AFR AF: 0.644

Gnomad AMI AF: 0.733

Gnomad AMR AF: 0.683

Gnomad ASJ AF: 0.642

Gnomad EAS AF: 0.815

Gnomad SAS AF: 0.697

Gnomad FIN AF: 0.582

Gnomad MID AF: 0.669

Gnomad NFE AF: 0.565

Gnomad OTH AF: 0.671

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

GnomAD4 genome AF: 0.617 AC: 93722 AN: 151950 Hom.: 29338 Cov.: 32 AF XY: 0.622 AC XY: 46214 AN XY: 74266

Gnomad4 AFR AF: 0.644

Gnomad4 AMR AF: 0.683

Gnomad4 ASJ AF: 0.642

Gnomad4 EAS AF: 0.814

Gnomad4 SAS AF: 0.697

Gnomad4 FIN AF: 0.582

Gnomad4 NFE AF: 0.565

Gnomad4 OTH AF: 0.676

Alfa AF: 0.589 Hom.: 10166

Bravo AF: 0.630

Asia WGS AF: 0.725 AC: 2515 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	2.9
DANN	Benign	0.38

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9276490; hg19: chr6-32718681;