rs9275424

Variant names:

• chr6-32702799-A-G
• rs9275424

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 0.295 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
• Publications: 32 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.294 AC: 12184 AN: 41446

American (AMR) AF: 0.397 AC: 6069 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.324 AC: 1123 AN: 3466

East Asian (EAS) AF: 0.298 AC: 1539 AN: 5170

South Asian (SAS) AF: 0.212 AC: 1022 AN: 4818

European-Finnish (FIN) AF: 0.466 AC: 4905 AN: 10534

Middle Eastern (MID) AF: 0.207 AC: 61 AN: 294

European-Non Finnish (NFE) AF: 0.249 AC: 16953 AN: 67986

Other (OTH) AF: 0.289 AC: 610 AN: 2114

Alfa AF: 0.304 Hom.: 8174

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
PhyloP100		-0.33

Splicing

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

Other links and lift over

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