rs963950

Variant names:

• chr21-33144401-C-T
• rs963950

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 0.0856 in 152,116 control chromosomes in the GnomAD database, including 705 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 0.086 (705 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00300
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.111 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: 0.0857 AC: 13029 AN: 151998 Hom.: 704 Cov.: 31

Gnomad AFR AF: 0.0296

Gnomad AMI AF: 0.126

Gnomad AMR AF: 0.105

Gnomad ASJ AF: 0.0386

Gnomad EAS AF: 0.101

Gnomad SAS AF: 0.104

Gnomad FIN AF: 0.0976

Gnomad MID AF: 0.0633

Gnomad NFE AF: 0.114

Gnomad OTH AF: 0.0781

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

GnomAD4 genome AF: 0.0856 AC: 13028 AN: 152116 Hom.: 705 Cov.: 31 AF XY: 0.0851 AC XY: 6327 AN XY: 74352

African (AFR) AF: 0.0295 AC: 1225 AN: 41524

American (AMR) AF: 0.105 AC: 1598 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.0386 AC: 134 AN: 3472

East Asian (EAS) AF: 0.101 AC: 522 AN: 5160

South Asian (SAS) AF: 0.104 AC: 502 AN: 4822

European-Finnish (FIN) AF: 0.0976 AC: 1031 AN: 10568

Middle Eastern (MID) AF: 0.0680 AC: 20 AN: 294

European-Non Finnish (NFE) AF: 0.114 AC: 7719 AN: 67978

Other (OTH) AF: 0.0769 AC: 162 AN: 2108

Alfa AF: 0.0946 Hom.: 1165

Bravo AF: 0.0820

Asia WGS AF: 0.0850 AC: 296 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	4.9
DANN	Benign	0.68
PhyloP100		0.0030

Splicing

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

Other links and lift over

dbSNP: rs963950; hg19: chr21-34516707;