6-55929595-C-T

Variant names:

• chr6-55929595-C-T
• rs10498809

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.0705 AC: 2916 AN: 41376

American (AMR) AF: 0.101 AC: 1536 AN: 15218

Ashkenazi Jewish (ASJ) AF: 0.0735 AC: 255 AN: 3468

East Asian (EAS) AF: 0.0483 AC: 250 AN: 5174

South Asian (SAS) AF: 0.0499 AC: 240 AN: 4810

European-Finnish (FIN) AF: 0.0583 AC: 615 AN: 10542

Middle Eastern (MID) AF: 0.0918 AC: 27 AN: 294

European-Non Finnish (NFE) AF: 0.0514 AC: 3495 AN: 67968

Other (OTH) AF: 0.0518 AC: 109 AN: 2104

Alfa AF: 0.0567 Hom.: 134

Bravo AF: 0.0660

Asia WGS AF: 0.0510 AC: 179 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.57
DANN	Benign	0.44
PhyloP100		-0.096

Splicing

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

Other links and lift over

dbSNP: rs10498809; hg19: chr6-55794393;