chr21-20816417-C-T

Variant names:

• chr21-20816417-C-T
• rs2826538

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 0.773 in 152,096 control chromosomes in the GnomAD database, including 45,627 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 0.77 (45627 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.05
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.86 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: 0.773 AC: 117505 AN: 151976 Hom.: 45586 Cov.: 32

Gnomad AFR AF: 0.802

Gnomad AMI AF: 0.818

Gnomad AMR AF: 0.803

Gnomad ASJ AF: 0.633

Gnomad EAS AF: 0.881

Gnomad SAS AF: 0.858

Gnomad FIN AF: 0.775

Gnomad MID AF: 0.832

Gnomad NFE AF: 0.741

Gnomad OTH AF: 0.760

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

GnomAD4 genome AF: 0.773 AC: 117601 AN: 152096 Hom.: 45627 Cov.: 32 AF XY: 0.778 AC XY: 57837 AN XY: 74340

African (AFR) AF: 0.802 AC: 33257 AN: 41460

American (AMR) AF: 0.804 AC: 12294 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.633 AC: 2196 AN: 3470

East Asian (EAS) AF: 0.882 AC: 4563 AN: 5176

South Asian (SAS) AF: 0.858 AC: 4138 AN: 4824

European-Finnish (FIN) AF: 0.775 AC: 8189 AN: 10560

Middle Eastern (MID) AF: 0.816 AC: 240 AN: 294

European-Non Finnish (NFE) AF: 0.741 AC: 50383 AN: 67996

Other (OTH) AF: 0.758 AC: 1597 AN: 2106

Alfa AF: 0.751 Hom.: 165091

Bravo AF: 0.777

Asia WGS AF: 0.839 AC: 2917 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.12
DANN	Benign	0.65
PhyloP100		-2.1

Splicing

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

Other links and lift over

dbSNP: rs2826538; hg19: chr21-22188735;