chr6-32699342-T-C

Position:

• chr6-32699342-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 0.763 in 152,068 control chromosomes in the GnomAD database, including 44,506 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 0.76 (44506 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -4.04

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.884 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: 0.763 AC: 115962 AN: 151950 Hom.: 44475 Cov.: 31

Gnomad AFR AF: 0.720

Gnomad AMI AF: 0.841

Gnomad AMR AF: 0.813

Gnomad ASJ AF: 0.843

Gnomad EAS AF: 0.906

Gnomad SAS AF: 0.881

Gnomad FIN AF: 0.753

Gnomad MID AF: 0.883

Gnomad NFE AF: 0.753

Gnomad OTH AF: 0.797

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

GnomAD4 genome AF: 0.763 AC: 116052 AN: 152068 Hom.: 44506 Cov.: 31 AF XY: 0.765 AC XY: 56882 AN XY: 74346

Gnomad4 AFR AF: 0.720

Gnomad4 AMR AF: 0.814

Gnomad4 ASJ AF: 0.843

Gnomad4 EAS AF: 0.906

Gnomad4 SAS AF: 0.881

Gnomad4 FIN AF: 0.753

Gnomad4 NFE AF: 0.753

Gnomad4 OTH AF: 0.799

Alfa AF: 0.762 Hom.: 35128

Bravo AF: 0.767

Asia WGS AF: 0.886 AC: 3081 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.39
DANN	Benign	0.38

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3135006; hg19: chr6-32667119;