chr6-213426-T-C

Variant names:

• chr6-213426-T-C
• rs6596836

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 0.411 in 151,898 control chromosomes in the GnomAD database, including 15,624 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 0.41 (15624 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.33
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.696 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.411 AC: 62370 AN: 151780 Hom.: 15591 Cov.: 31

Gnomad AFR AF: 0.702

Gnomad AMI AF: 0.236

Gnomad AMR AF: 0.354

Gnomad ASJ AF: 0.329

Gnomad EAS AF: 0.608

Gnomad SAS AF: 0.292

Gnomad FIN AF: 0.267

Gnomad MID AF: 0.296

Gnomad NFE AF: 0.270

Gnomad OTH AF: 0.398

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

GnomAD4 genome AF: 0.411 AC: 62468 AN: 151898 Hom.: 15624 Cov.: 31 AF XY: 0.410 AC XY: 30440 AN XY: 74226

African (AFR) AF: 0.703 AC: 29078 AN: 41378

American (AMR) AF: 0.355 AC: 5421 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.329 AC: 1142 AN: 3466

East Asian (EAS) AF: 0.608 AC: 3126 AN: 5144

South Asian (SAS) AF: 0.288 AC: 1384 AN: 4812

European-Finnish (FIN) AF: 0.267 AC: 2817 AN: 10554

Middle Eastern (MID) AF: 0.308 AC: 90 AN: 292

European-Non Finnish (NFE) AF: 0.270 AC: 18349 AN: 67950

Other (OTH) AF: 0.401 AC: 846 AN: 2108

Alfa AF: 0.308 Hom.: 13168

Bravo AF: 0.431

Asia WGS AF: 0.486 AC: 1689 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.64
DANN	Benign	0.23
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs6596836; hg19: chr6-213426;