6-142226962-C-T

Variant names:

• chr6-142226962-C-T
• rs225717

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 0.81 in 152,056 control chromosomes in the GnomAD database, including 50,376 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 0.81 (50376 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0900
• Publications: 19 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 (EAS) allele frequency at 95% confidence interval = 0.899 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.810 AC: 123111 AN: 151940 Hom.: 50312 Cov.: 31

Gnomad AFR AF: 0.897

Gnomad AMI AF: 0.631

Gnomad AMR AF: 0.766

Gnomad ASJ AF: 0.814

Gnomad EAS AF: 0.921

Gnomad SAS AF: 0.735

Gnomad FIN AF: 0.859

Gnomad MID AF: 0.804

Gnomad NFE AF: 0.760

Gnomad OTH AF: 0.788

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

GnomAD4 genome AF: 0.810 AC: 123229 AN: 152056 Hom.: 50376 Cov.: 31 AF XY: 0.812 AC XY: 60328 AN XY: 74312

African (AFR) AF: 0.897 AC: 37193 AN: 41474

American (AMR) AF: 0.766 AC: 11684 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.814 AC: 2826 AN: 3470

East Asian (EAS) AF: 0.921 AC: 4765 AN: 5172

South Asian (SAS) AF: 0.735 AC: 3539 AN: 4814

European-Finnish (FIN) AF: 0.859 AC: 9097 AN: 10594

Middle Eastern (MID) AF: 0.803 AC: 236 AN: 294

European-Non Finnish (NFE) AF: 0.760 AC: 51643 AN: 67952

Other (OTH) AF: 0.791 AC: 1672 AN: 2114

Alfa AF: 0.775 Hom.: 144658

Bravo AF: 0.807

Asia WGS AF: 0.811 AC: 2823 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	3.2
DANN	Benign	0.70
PhyloP100		0.090

Splicing

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

Other links and lift over

dbSNP: rs225717; hg19: chr6-142548099;