6-55929595-C-T

Position:

• chr6-55929595-C-T

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 0.0624 in 151,862 control chromosomes in the GnomAD database, including 351 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 0.062 (351 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0960

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.0967 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: 0.0624 AC: 9465 AN: 151746 Hom.: 351 Cov.: 31

Gnomad AFR AF: 0.0704

Gnomad AMI AF: 0.0374

Gnomad AMR AF: 0.101

Gnomad ASJ AF: 0.0735

Gnomad EAS AF: 0.0484

Gnomad SAS AF: 0.0499

Gnomad FIN AF: 0.0583

Gnomad MID AF: 0.0949

Gnomad NFE AF: 0.0514

Gnomad OTH AF: 0.0524

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

GnomAD4 genome AF: 0.0624 AC: 9477 AN: 151862 Hom.: 351 Cov.: 31 AF XY: 0.0624 AC XY: 4632 AN XY: 74212

Gnomad4 AFR AF: 0.0705

Gnomad4 AMR AF: 0.101

Gnomad4 ASJ AF: 0.0735

Gnomad4 EAS AF: 0.0483

Gnomad4 SAS AF: 0.0499

Gnomad4 FIN AF: 0.0583

Gnomad4 NFE AF: 0.0514

Gnomad4 OTH AF: 0.0518

Alfa AF: 0.0566 Hom.: 118

Bravo AF: 0.0660

Asia WGS AF: 0.0510 AC: 179 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.57
DANN	Benign	0.44

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10498809; hg19: chr6-55794393;