6-32420769-T-C

Position:

• chr6-32420769-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 0.805 in 152,186 control chromosomes in the GnomAD database, including 49,537 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 0.80 (49537 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.05

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.954 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: 0.805 AC: 122364 AN: 152068 Hom.: 49505 Cov.: 32

Gnomad AFR AF: 0.769

Gnomad AMI AF: 0.863

Gnomad AMR AF: 0.817

Gnomad ASJ AF: 0.899

Gnomad EAS AF: 0.976

Gnomad SAS AF: 0.928

Gnomad FIN AF: 0.859

Gnomad MID AF: 0.877

Gnomad NFE AF: 0.787

Gnomad OTH AF: 0.809

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

GnomAD4 genome AF: 0.805 AC: 122448 AN: 152186 Hom.: 49537 Cov.: 32 AF XY: 0.810 AC XY: 60282 AN XY: 74406

Gnomad4 AFR AF: 0.769

Gnomad4 AMR AF: 0.817

Gnomad4 ASJ AF: 0.899

Gnomad4 EAS AF: 0.976

Gnomad4 SAS AF: 0.928

Gnomad4 FIN AF: 0.859

Gnomad4 NFE AF: 0.787

Gnomad4 OTH AF: 0.812

Alfa AF: 0.795 Hom.: 15236

Bravo AF: 0.797

Asia WGS AF: 0.922 AC: 3204 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.11
DANN	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2213581; hg19: chr6-32388546;