rs9275424

Variant names:

• chr6-32702799-A-G
• rs9275424

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 0.295 in 152,016 control chromosomes in the GnomAD database, including 7,034 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 0.29 (7034 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.327

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.389 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: 0.295 AC: 44764 AN: 151898 Hom.: 7018 Cov.: 32

Gnomad AFR AF: 0.294

Gnomad AMI AF: 0.396

Gnomad AMR AF: 0.396

Gnomad ASJ AF: 0.324

Gnomad EAS AF: 0.297

Gnomad SAS AF: 0.210

Gnomad FIN AF: 0.466

Gnomad MID AF: 0.203

Gnomad NFE AF: 0.249

Gnomad OTH AF: 0.291

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

GnomAD4 genome AF: 0.295 AC: 44825 AN: 152016 Hom.: 7034 Cov.: 32 AF XY: 0.305 AC XY: 22631 AN XY: 74306

Gnomad4 AFR AF: 0.294

Gnomad4 AMR AF: 0.397

Gnomad4 ASJ AF: 0.324

Gnomad4 EAS AF: 0.298

Gnomad4 SAS AF: 0.212

Gnomad4 FIN AF: 0.466

Gnomad4 NFE AF: 0.249

Gnomad4 OTH AF: 0.289

Alfa AF: 0.263 Hom.: 2613

Bravo AF: 0.295

Asia WGS AF: 0.276 AC: 965 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	4.5
DANN	Benign	0.34

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9275424; hg19: chr6-32670576; COSMIC: COSV70582377;