rs200681

chr21-23337020-C-Tchr21-23337020-C-Achr21-23337020-C-G

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;