6-32249408-T-C

Position:

• chr6-32249408-T-C

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 0.415 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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.342

Gnomad4 AMR AF: 0.513

Gnomad4 ASJ AF: 0.641

Gnomad4 EAS AF: 0.474

Gnomad4 SAS AF: 0.574

Gnomad4 FIN AF: 0.275

Gnomad4 NFE AF: 0.430

Gnomad4 OTH AF: 0.447

Alfa AF: 0.423 Hom.: 1940

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9267971; hg19: chr6-32217185;