rs3814903

Variant names:

• chr21-42397008-G-T
• rs3814903

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 0.36 in 151,950 control chromosomes in the GnomAD database, including 10,065 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 0.36 (10065 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -4.09
• Publications: 11 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.07).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.404 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: 0.360 AC: 54618 AN: 151832 Hom.: 10049 Cov.: 31

Gnomad AFR AF: 0.409

Gnomad AMI AF: 0.335

Gnomad AMR AF: 0.291

Gnomad ASJ AF: 0.410

Gnomad EAS AF: 0.367

Gnomad SAS AF: 0.277

Gnomad FIN AF: 0.387

Gnomad MID AF: 0.326

Gnomad NFE AF: 0.344

Gnomad OTH AF: 0.362

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

GnomAD4 genome AF: 0.360 AC: 54677 AN: 151950 Hom.: 10065 Cov.: 31 AF XY: 0.358 AC XY: 26589 AN XY: 74278

African (AFR) AF: 0.409 AC: 16942 AN: 41404

American (AMR) AF: 0.291 AC: 4443 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.410 AC: 1422 AN: 3470

East Asian (EAS) AF: 0.367 AC: 1899 AN: 5172

South Asian (SAS) AF: 0.276 AC: 1327 AN: 4810

European-Finnish (FIN) AF: 0.387 AC: 4079 AN: 10550

Middle Eastern (MID) AF: 0.320 AC: 94 AN: 294

European-Non Finnish (NFE) AF: 0.344 AC: 23394 AN: 67952

Other (OTH) AF: 0.367 AC: 772 AN: 2106

Alfa AF: 0.342 Hom.: 16739

Bravo AF: 0.357

Asia WGS AF: 0.382 AC: 1326 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.0020
DANN	Benign	0.59
PhyloP100		-4.1

Splicing

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

Other links and lift over

dbSNP: rs3814903; hg19: chr21-43817117;