6-32249408-T-C

Variant names:

• chr6-32249408-T-C
• rs9267971

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 0.415 in 151,906 control chromosomes in the GnomAD database, including 13,599 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 0.41 (13599 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.214
• Publications: 9 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.556 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: 0.415 AC: 62977 AN: 151788 Hom.: 13589 Cov.: 31

Gnomad AFR AF: 0.343

Gnomad AMI AF: 0.407

Gnomad AMR AF: 0.512

Gnomad ASJ AF: 0.641

Gnomad EAS AF: 0.473

Gnomad SAS AF: 0.573

Gnomad FIN AF: 0.275

Gnomad MID AF: 0.633

Gnomad NFE AF: 0.430

Gnomad OTH AF: 0.450

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

GnomAD4 genome AF: 0.415 AC: 63010 AN: 151906 Hom.: 13599 Cov.: 31 AF XY: 0.414 AC XY: 30717 AN XY: 74256

African (AFR) AF: 0.342 AC: 14180 AN: 41402

American (AMR) AF: 0.513 AC: 7822 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.641 AC: 2219 AN: 3464

East Asian (EAS) AF: 0.474 AC: 2441 AN: 5154

South Asian (SAS) AF: 0.574 AC: 2757 AN: 4804

European-Finnish (FIN) AF: 0.275 AC: 2912 AN: 10576

Middle Eastern (MID) AF: 0.629 AC: 185 AN: 294

European-Non Finnish (NFE) AF: 0.430 AC: 29182 AN: 67932

Other (OTH) AF: 0.447 AC: 942 AN: 2108

Alfa AF: 0.417 Hom.: 5497

Bravo AF: 0.428

Asia WGS AF: 0.470 AC: 1638 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	7.6
DANN	Benign	0.59
PhyloP100		0.21

Splicing

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

Other links and lift over

dbSNP: rs9267971; hg19: chr6-32217185;