chr6-63093283-C-A

Position:

• chr6-63093283-C-A

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 0.728 in 152,054 control chromosomes in the GnomAD database, including 40,613 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 0.73 (40613 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.360

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 = 0.761 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: 0.728 AC: 110648 AN: 151936 Hom.: 40598 Cov.: 32

Gnomad AFR AF: 0.768

Gnomad AMI AF: 0.740

Gnomad AMR AF: 0.666

Gnomad ASJ AF: 0.708

Gnomad EAS AF: 0.670

Gnomad SAS AF: 0.577

Gnomad FIN AF: 0.834

Gnomad MID AF: 0.750

Gnomad NFE AF: 0.718

Gnomad OTH AF: 0.720

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

GnomAD4 genome AF: 0.728 AC: 110705 AN: 152054 Hom.: 40613 Cov.: 32 AF XY: 0.728 AC XY: 54076 AN XY: 74320

Gnomad4 AFR AF: 0.768

Gnomad4 AMR AF: 0.665

Gnomad4 ASJ AF: 0.708

Gnomad4 EAS AF: 0.670

Gnomad4 SAS AF: 0.577

Gnomad4 FIN AF: 0.834

Gnomad4 NFE AF: 0.718

Gnomad4 OTH AF: 0.716

Alfa AF: 0.712 Hom.: 35877

Bravo AF: 0.720

Asia WGS AF: 0.584 AC: 2033 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.3
DANN	Benign	0.53

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs789942; hg19: chr6-63803188;