chr21-13266595-T-C

Variant names:

• chr21-13266595-T-C
• rs2742158

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 0.576 in 151,922 control chromosomes in the GnomAD database, including 25,779 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 0.58 (25779 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.342
• Publications: 0 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 (EAS) allele frequency at 95% confidence interval = 0.754 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: 0.576 AC: 87440 AN: 151804 Hom.: 25735 Cov.: 32

Gnomad AFR AF: 0.635

Gnomad AMI AF: 0.462

Gnomad AMR AF: 0.631

Gnomad ASJ AF: 0.615

Gnomad EAS AF: 0.775

Gnomad SAS AF: 0.555

Gnomad FIN AF: 0.499

Gnomad MID AF: 0.601

Gnomad NFE AF: 0.525

Gnomad OTH AF: 0.589

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

GnomAD4 genome AF: 0.576 AC: 87546 AN: 151922 Hom.: 25779 Cov.: 32 AF XY: 0.575 AC XY: 42725 AN XY: 74258

African (AFR) AF: 0.636 AC: 26339 AN: 41426

American (AMR) AF: 0.631 AC: 9625 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.615 AC: 2134 AN: 3472

East Asian (EAS) AF: 0.774 AC: 3981 AN: 5142

South Asian (SAS) AF: 0.556 AC: 2680 AN: 4824

European-Finnish (FIN) AF: 0.499 AC: 5273 AN: 10570

Middle Eastern (MID) AF: 0.605 AC: 178 AN: 294

European-Non Finnish (NFE) AF: 0.525 AC: 35666 AN: 67920

Other (OTH) AF: 0.592 AC: 1251 AN: 2114

Alfa AF: 0.543 Hom.: 2967

Bravo AF: 0.592

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	8.5
DANN	Benign	0.55
PhyloP100		0.34

Splicing

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

Other links and lift over

dbSNP: rs2742158; hg19: chr21-14638916;