6-32988943-T-C

Position:

• chr6-32988943-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 0.635 in 151,826 control chromosomes in the GnomAD database, including 31,887 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 0.64 (31887 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.531

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.823 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: 0.635 AC: 96331 AN: 151708 Hom.: 31836 Cov.: 30

Gnomad AFR AF: 0.830

Gnomad AMI AF: 0.508

Gnomad AMR AF: 0.541

Gnomad ASJ AF: 0.607

Gnomad EAS AF: 0.478

Gnomad SAS AF: 0.483

Gnomad FIN AF: 0.613

Gnomad MID AF: 0.642

Gnomad NFE AF: 0.567

Gnomad OTH AF: 0.636

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

GnomAD4 genome AF: 0.635 AC: 96432 AN: 151826 Hom.: 31887 Cov.: 30 AF XY: 0.631 AC XY: 46819 AN XY: 74226

Gnomad4 AFR AF: 0.830

Gnomad4 AMR AF: 0.540

Gnomad4 ASJ AF: 0.607

Gnomad4 EAS AF: 0.479

Gnomad4 SAS AF: 0.481

Gnomad4 FIN AF: 0.613

Gnomad4 NFE AF: 0.567

Gnomad4 OTH AF: 0.633

Alfa AF: 0.620 Hom.: 3759

Bravo AF: 0.639

Asia WGS AF: 0.514 AC: 1788 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	6.4
DANN	Benign	0.77

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs497058; hg19: chr6-32956720; COSMIC: COSV53487862;