chr21-39808149-A-G

Variant names:

• chr21-39808149-A-G
• rs2410182

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 0.711 in 151,868 control chromosomes in the GnomAD database, including 40,030 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 0.71 (40030 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.44
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.904 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: 0.710 AC: 107809 AN: 151750 Hom.: 39966 Cov.: 31

Gnomad AFR AF: 0.912

Gnomad AMI AF: 0.613

Gnomad AMR AF: 0.751

Gnomad ASJ AF: 0.647

Gnomad EAS AF: 0.874

Gnomad SAS AF: 0.829

Gnomad FIN AF: 0.584

Gnomad MID AF: 0.686

Gnomad NFE AF: 0.582

Gnomad OTH AF: 0.719

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

GnomAD4 genome AF: 0.711 AC: 107935 AN: 151868 Hom.: 40030 Cov.: 31 AF XY: 0.714 AC XY: 52995 AN XY: 74204

African (AFR) AF: 0.912 AC: 37816 AN: 41480

American (AMR) AF: 0.752 AC: 11461 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.647 AC: 2247 AN: 3472

East Asian (EAS) AF: 0.874 AC: 4496 AN: 5142

South Asian (SAS) AF: 0.828 AC: 3990 AN: 4816

European-Finnish (FIN) AF: 0.584 AC: 6135 AN: 10506

Middle Eastern (MID) AF: 0.703 AC: 204 AN: 290

European-Non Finnish (NFE) AF: 0.582 AC: 39506 AN: 67894

Other (OTH) AF: 0.721 AC: 1522 AN: 2112

Alfa AF: 0.635 Hom.: 21120

Bravo AF: 0.731

Asia WGS AF: 0.865 AC: 3007 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.2
DANN	Benign	0.47
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs2410182; hg19: chr21-41180076;