rs9275374

Variant names:

• chr6-32700749-C-T
• rs9275374

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 152,072 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
• Publications: 27 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.389 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.294 AC: 12197 AN: 41476

American (AMR) AF: 0.398 AC: 6077 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.325 AC: 1127 AN: 3470

East Asian (EAS) AF: 0.297 AC: 1542 AN: 5186

South Asian (SAS) AF: 0.212 AC: 1023 AN: 4824

European-Finnish (FIN) AF: 0.466 AC: 4921 AN: 10552

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

European-Non Finnish (NFE) AF: 0.249 AC: 16950 AN: 67974

Other (OTH) AF: 0.289 AC: 609 AN: 2104

Alfa AF: 0.274 Hom.: 5638

Bravo AF: 0.295

Asia WGS AF: 0.277 AC: 970 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	9.1
DANN	Benign	0.45
PhyloP100		-1.4

Splicing

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

Other links and lift over

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