rs2173962

Variant names:

• chr21-31649707-T-C
• rs2173962

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 0.0705 in 152,028 control chromosomes in the GnomAD database, including 508 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 0.070 (508 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.114

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.69).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.134 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: 0.0703 AC: 10676 AN: 151910 Hom.: 501 Cov.: 31

Gnomad AFR AF: 0.136

Gnomad AMI AF: 0.0495

Gnomad AMR AF: 0.0345

Gnomad ASJ AF: 0.0156

Gnomad EAS AF: 0.00212

Gnomad SAS AF: 0.0108

Gnomad FIN AF: 0.0952

Gnomad MID AF: 0.0158

Gnomad NFE AF: 0.0475

Gnomad OTH AF: 0.0540

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

GnomAD4 genome AF: 0.0705 AC: 10715 AN: 152028 Hom.: 508 Cov.: 31 AF XY: 0.0713 AC XY: 5295 AN XY: 74284

Gnomad4 AFR AF: 0.137

Gnomad4 AMR AF: 0.0344

Gnomad4 ASJ AF: 0.0156

Gnomad4 EAS AF: 0.00212

Gnomad4 SAS AF: 0.0110

Gnomad4 FIN AF: 0.0952

Gnomad4 NFE AF: 0.0475

Gnomad4 OTH AF: 0.0539

Alfa AF: 0.0640 Hom.: 79

Bravo AF: 0.0687

Asia WGS AF: 0.0200 AC: 71 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.69
CADD	Benign	13
DANN	Benign	0.96

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2173962; hg19: chr21-33022020;