21-44987477-T-C

Variant names:

• chr21-44987477-T-C
• rs9974719

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 0.565 in 151,996 control chromosomes in the GnomAD database, including 24,580 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 0.57 (24580 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.02
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.684 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.565 AC: 85874 AN: 151878 Hom.: 24572 Cov.: 32

Gnomad AFR AF: 0.514

Gnomad AMI AF: 0.549

Gnomad AMR AF: 0.577

Gnomad ASJ AF: 0.516

Gnomad EAS AF: 0.664

Gnomad SAS AF: 0.702

Gnomad FIN AF: 0.607

Gnomad MID AF: 0.611

Gnomad NFE AF: 0.573

Gnomad OTH AF: 0.574

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

GnomAD4 genome AF: 0.565 AC: 85930 AN: 151996 Hom.: 24580 Cov.: 32 AF XY: 0.567 AC XY: 42142 AN XY: 74284

African (AFR) AF: 0.513 AC: 21263 AN: 41414

American (AMR) AF: 0.577 AC: 8821 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.516 AC: 1790 AN: 3472

East Asian (EAS) AF: 0.664 AC: 3431 AN: 5168

South Asian (SAS) AF: 0.704 AC: 3396 AN: 4826

European-Finnish (FIN) AF: 0.607 AC: 6429 AN: 10584

Middle Eastern (MID) AF: 0.619 AC: 182 AN: 294

European-Non Finnish (NFE) AF: 0.573 AC: 38914 AN: 67936

Other (OTH) AF: 0.574 AC: 1208 AN: 2106

Alfa AF: 0.570 Hom.: 4949

Bravo AF: 0.558

Asia WGS AF: 0.665 AC: 2310 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.1
DANN	Benign	0.31
PhyloP100		-3.0

Splicing

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

Other links and lift over

dbSNP: rs9974719; hg19: chr21-46407392;