21-23337020-C-T

Variant names:

• chr21-23337020-C-T
• rs200681

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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

Gnomad4 AFR AF: 0.601

Gnomad4 AMR AF: 0.725

Gnomad4 ASJ AF: 0.708

Gnomad4 EAS AF: 0.664

Gnomad4 SAS AF: 0.760

Gnomad4 FIN AF: 0.718

Gnomad4 NFE AF: 0.739

Gnomad4 OTH AF: 0.706

Alfa AF: 0.609 Hom.: 2242

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs200681; hg19: chr21-24709342;