21-44981317-T-C

Variant names:

• chr21-44981317-T-C
• rs914203

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 0.803 in 152,288 control chromosomes in the GnomAD database, including 49,250 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 0.80 (49250 hom., cov: 37)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.26
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.829 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.803 AC: 122239 AN: 152170 Hom.: 49210 Cov.: 37

Gnomad AFR AF: 0.837

Gnomad AMI AF: 0.768

Gnomad AMR AF: 0.817

Gnomad ASJ AF: 0.753

Gnomad EAS AF: 0.832

Gnomad SAS AF: 0.827

Gnomad FIN AF: 0.790

Gnomad MID AF: 0.775

Gnomad NFE AF: 0.781

Gnomad OTH AF: 0.801

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

GnomAD4 genome AF: 0.803 AC: 122338 AN: 152288 Hom.: 49250 Cov.: 37 AF XY: 0.803 AC XY: 59770 AN XY: 74462

African (AFR) AF: 0.837 AC: 34779 AN: 41562

American (AMR) AF: 0.817 AC: 12504 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.753 AC: 2613 AN: 3470

East Asian (EAS) AF: 0.832 AC: 4301 AN: 5172

South Asian (SAS) AF: 0.827 AC: 3998 AN: 4832

European-Finnish (FIN) AF: 0.790 AC: 8384 AN: 10614

Middle Eastern (MID) AF: 0.776 AC: 228 AN: 294

European-Non Finnish (NFE) AF: 0.781 AC: 53133 AN: 68014

Other (OTH) AF: 0.802 AC: 1698 AN: 2116

Alfa AF: 0.769 Hom.: 5877

Bravo AF: 0.804

Asia WGS AF: 0.839 AC: 2917 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.93
DANN	Benign	0.19
PhyloP100		-2.3

Splicing

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

Other links and lift over

dbSNP: rs914203; hg19: chr21-46401232; COSMIC: COSV52422377;