6-32446496-T-C

Position:

• chr6-32446496-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 0.292 in 149,974 control chromosomes in the GnomAD database, including 6,645 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 (6645 hom., cov: 28)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.547

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.353 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.292 AC: 43787 AN: 149888 Hom.: 6631 Cov.: 28

Gnomad AFR AF: 0.357

Gnomad AMI AF: 0.127

Gnomad AMR AF: 0.259

Gnomad ASJ AF: 0.220

Gnomad EAS AF: 0.311

Gnomad SAS AF: 0.252

Gnomad FIN AF: 0.341

Gnomad MID AF: 0.237

Gnomad NFE AF: 0.261

Gnomad OTH AF: 0.288

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

GnomAD4 genome AF: 0.292 AC: 43838 AN: 149974 Hom.: 6645 Cov.: 28 AF XY: 0.292 AC XY: 21330 AN XY: 73070

Gnomad4 AFR AF: 0.357

Gnomad4 AMR AF: 0.260

Gnomad4 ASJ AF: 0.220

Gnomad4 EAS AF: 0.311

Gnomad4 SAS AF: 0.252

Gnomad4 FIN AF: 0.341

Gnomad4 NFE AF: 0.261

Gnomad4 OTH AF: 0.291

Alfa AF: 0.264 Hom.: 9482

Bravo AF: 0.291

Asia WGS AF: 0.325 AC: 1129 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.0
DANN	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3129890; hg19: chr6-32414273;