21-41044096-T-C

Variant names:

• chr21-41044096-T-C
• rs914166

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 0.844 in 152,182 control chromosomes in the GnomAD database, including 55,094 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 0.84 (55094 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.23
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.954 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: 0.844 AC: 128322 AN: 152064 Hom.: 55044 Cov.: 32

Gnomad AFR AF: 0.962

Gnomad AMI AF: 0.885

Gnomad AMR AF: 0.776

Gnomad ASJ AF: 0.783

Gnomad EAS AF: 0.450

Gnomad SAS AF: 0.775

Gnomad FIN AF: 0.739

Gnomad MID AF: 0.826

Gnomad NFE AF: 0.841

Gnomad OTH AF: 0.833

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

GnomAD4 genome AF: 0.844 AC: 128430 AN: 152182 Hom.: 55094 Cov.: 32 AF XY: 0.833 AC XY: 61989 AN XY: 74392

African (AFR) AF: 0.962 AC: 39970 AN: 41534

American (AMR) AF: 0.776 AC: 11863 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.783 AC: 2717 AN: 3470

East Asian (EAS) AF: 0.450 AC: 2320 AN: 5158

South Asian (SAS) AF: 0.774 AC: 3733 AN: 4822

European-Finnish (FIN) AF: 0.739 AC: 7820 AN: 10578

Middle Eastern (MID) AF: 0.816 AC: 240 AN: 294

European-Non Finnish (NFE) AF: 0.841 AC: 57201 AN: 68008

Other (OTH) AF: 0.832 AC: 1761 AN: 2116

Alfa AF: 0.839 Hom.: 29128

Bravo AF: 0.851

Asia WGS AF: 0.673 AC: 2344 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	0.15
DANN	Benign	0.45
PhyloP100		-2.2

Splicing

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

Other links and lift over

dbSNP: rs914166; hg19: chr21-42416022;