rs9275374

Positions:

• chr6-32700749-C-T

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 152,072 control chromosomes in the GnomAD database, including 7,067 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 0.30 (7067 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.43

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• 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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.295 AC: 44809 AN: 151952 Hom.: 7050 Cov.: 32

Gnomad AFR AF: 0.294

Gnomad AMI AF: 0.400

Gnomad AMR AF: 0.397

Gnomad ASJ AF: 0.325

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: 0.292

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

GnomAD4 genome AF: 0.295 AC: 44872 AN: 152072 Hom.: 7067 Cov.: 32 AF XY: 0.305 AC XY: 22663 AN XY: 74316

Gnomad4 AFR AF: 0.294

Gnomad4 AMR AF: 0.398

Gnomad4 ASJ AF: 0.325

Gnomad4 EAS AF: 0.297

Gnomad4 SAS AF: 0.212

Gnomad4 FIN AF: 0.466

Gnomad4 NFE AF: 0.249

Gnomad4 OTH AF: 0.289

Alfa AF: 0.270 Hom.: 3443

Bravo AF: 0.295

Asia WGS AF: 0.277 AC: 970 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	9.1
DANN	Benign	0.45

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9275374; hg19: chr6-32668526; COSMIC: COSV56048229;