rs2173962

Positions:

• chr21-31649707-T-C

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/exons	MANE	UniProt

Ensembl

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