chr21-23337020-C-T

Variant names:

• chr21-23337020-C-T
• rs200681

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 0.695 in 151,970 control chromosomes in the GnomAD database, including 37,026 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 0.69 (37026 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.921
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.739 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: 0.695 AC: 105499 AN: 151852 Hom.: 37003 Cov.: 31

Gnomad AFR AF: 0.601

Gnomad AMI AF: 0.612

Gnomad AMR AF: 0.726

Gnomad ASJ AF: 0.708

Gnomad EAS AF: 0.664

Gnomad SAS AF: 0.761

Gnomad FIN AF: 0.718

Gnomad MID AF: 0.710

Gnomad NFE AF: 0.739

Gnomad OTH AF: 0.703

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

GnomAD4 genome AF: 0.695 AC: 105578 AN: 151970 Hom.: 37026 Cov.: 31 AF XY: 0.694 AC XY: 51512 AN XY: 74274

African (AFR) AF: 0.601 AC: 24898 AN: 41420

American (AMR) AF: 0.725 AC: 11082 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.708 AC: 2458 AN: 3472

East Asian (EAS) AF: 0.664 AC: 3416 AN: 5146

South Asian (SAS) AF: 0.760 AC: 3661 AN: 4818

European-Finnish (FIN) AF: 0.718 AC: 7577 AN: 10558

Middle Eastern (MID) AF: 0.723 AC: 211 AN: 292

European-Non Finnish (NFE) AF: 0.739 AC: 50226 AN: 67966

Other (OTH) AF: 0.706 AC: 1492 AN: 2112

Alfa AF: 0.607 Hom.: 2380

Bravo AF: 0.695

Asia WGS AF: 0.734 AC: 2553 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.1
DANN	Benign	0.17
PhyloP100		-0.92

Splicing

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

Other links and lift over

dbSNP: rs200681; hg19: chr21-24709342;