rs9275388

Variant names:

• chr6-32701307-T-C
• rs9275388

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 151,832 control chromosomes in the GnomAD database, including 7,058 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 (7058 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0510
• Publications: 27 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• 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: 44722 AN: 151714 Hom.: 7042 Cov.: 31

Gnomad AFR AF: 0.294

Gnomad AMI AF: 0.401

Gnomad AMR AF: 0.397

Gnomad ASJ AF: 0.324

Gnomad EAS AF: 0.296

Gnomad SAS AF: 0.211

Gnomad FIN AF: 0.466

Gnomad MID AF: 0.203

Gnomad NFE AF: 0.249

Gnomad OTH AF: 0.292

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

GnomAD4 genome AF: 0.295 AC: 44783 AN: 151832 Hom.: 7058 Cov.: 31 AF XY: 0.305 AC XY: 22617 AN XY: 74194

African (AFR) AF: 0.294 AC: 12173 AN: 41398

American (AMR) AF: 0.398 AC: 6070 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.324 AC: 1124 AN: 3466

East Asian (EAS) AF: 0.297 AC: 1531 AN: 5158

South Asian (SAS) AF: 0.212 AC: 1020 AN: 4802

European-Finnish (FIN) AF: 0.466 AC: 4894 AN: 10492

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

European-Non Finnish (NFE) AF: 0.249 AC: 16937 AN: 67942

Other (OTH) AF: 0.289 AC: 608 AN: 2102

Alfa AF: 0.270 Hom.: 5225

Bravo AF: 0.295

Asia WGS AF: 0.276 AC: 965 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	9.4
DANN	Benign	0.86
PhyloP100		0.051

Splicing

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

Other links and lift over

dbSNP: rs9275388; hg19: chr6-32669084;