21-44982680-G-A

Variant names:

• chr21-44982680-G-A
• rs34809169

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 0.146 in 152,286 control chromosomes in the GnomAD database, including 1,881 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 0.15 (1881 hom., cov: 35)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.553
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.229 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.146 AC: 22211 AN: 152168 Hom.: 1872 Cov.: 35

Gnomad AFR AF: 0.233

Gnomad AMI AF: 0.0757

Gnomad AMR AF: 0.107

Gnomad ASJ AF: 0.120

Gnomad EAS AF: 0.0867

Gnomad SAS AF: 0.0857

Gnomad FIN AF: 0.101

Gnomad MID AF: 0.174

Gnomad NFE AF: 0.119

Gnomad OTH AF: 0.150

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

GnomAD4 genome AF: 0.146 AC: 22245 AN: 152286 Hom.: 1881 Cov.: 35 AF XY: 0.142 AC XY: 10544 AN XY: 74466

African (AFR) AF: 0.233 AC: 9696 AN: 41546

American (AMR) AF: 0.107 AC: 1639 AN: 15306

Ashkenazi Jewish (ASJ) AF: 0.120 AC: 417 AN: 3468

East Asian (EAS) AF: 0.0867 AC: 450 AN: 5188

South Asian (SAS) AF: 0.0862 AC: 416 AN: 4826

European-Finnish (FIN) AF: 0.101 AC: 1078 AN: 10626

Middle Eastern (MID) AF: 0.180 AC: 53 AN: 294

European-Non Finnish (NFE) AF: 0.119 AC: 8108 AN: 68010

Other (OTH) AF: 0.151 AC: 319 AN: 2110

Alfa AF: 0.0637 Hom.: 72

Bravo AF: 0.151

Asia WGS AF: 0.112 AC: 389 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.3
DANN	Benign	0.84
PhyloP100		-0.55

Splicing

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

Other links and lift over

dbSNP: rs34809169; hg19: chr21-46402595; COSMIC: COSV69383643;