rs3814896

Variant names:

• chr21-42351602-A-G
• rs3814896

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 0.169 in 152,118 control chromosomes in the GnomAD database, including 2,645 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 0.17 (2645 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.448
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.223 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: 0.169 AC: 25656 AN: 152000 Hom.: 2645 Cov.: 32

Gnomad AFR AF: 0.0595

Gnomad AMI AF: 0.228

Gnomad AMR AF: 0.136

Gnomad ASJ AF: 0.169

Gnomad EAS AF: 0.149

Gnomad SAS AF: 0.233

Gnomad FIN AF: 0.246

Gnomad MID AF: 0.184

Gnomad NFE AF: 0.226

Gnomad OTH AF: 0.182

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

GnomAD4 genome AF: 0.169 AC: 25655 AN: 152118 Hom.: 2645 Cov.: 32 AF XY: 0.171 AC XY: 12728 AN XY: 74358

African (AFR) AF: 0.0593 AC: 2460 AN: 41506

American (AMR) AF: 0.136 AC: 2080 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.169 AC: 588 AN: 3470

East Asian (EAS) AF: 0.150 AC: 774 AN: 5172

South Asian (SAS) AF: 0.233 AC: 1123 AN: 4818

European-Finnish (FIN) AF: 0.246 AC: 2598 AN: 10570

Middle Eastern (MID) AF: 0.194 AC: 57 AN: 294

European-Non Finnish (NFE) AF: 0.226 AC: 15382 AN: 67974

Other (OTH) AF: 0.182 AC: 385 AN: 2112

Alfa AF: 0.197 Hom.: 5963

Bravo AF: 0.154

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	2.9
DANN	Benign	0.82
PhyloP100		0.45

Splicing

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

Other links and lift over

dbSNP: rs3814896; hg19: chr21-43771711;