rs3810427

Variant names:

• chr19-15935840-C-A
• rs3810427

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 0.385 in 151,940 control chromosomes in the GnomAD database, including 12,767 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 0.38 (12767 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.19
• Publications: 25 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.08).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.493 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: 0.385 AC: 58489 AN: 151822 Hom.: 12771 Cov.: 31

Gnomad AFR AF: 0.161

Gnomad AMI AF: 0.560

Gnomad AMR AF: 0.406

Gnomad ASJ AF: 0.421

Gnomad EAS AF: 0.425

Gnomad SAS AF: 0.510

Gnomad FIN AF: 0.479

Gnomad MID AF: 0.405

Gnomad NFE AF: 0.487

Gnomad OTH AF: 0.375

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

GnomAD4 genome AF: 0.385 AC: 58495 AN: 151940 Hom.: 12767 Cov.: 31 AF XY: 0.384 AC XY: 28546 AN XY: 74268

African (AFR) AF: 0.161 AC: 6663 AN: 41456

American (AMR) AF: 0.406 AC: 6191 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.421 AC: 1461 AN: 3470

East Asian (EAS) AF: 0.425 AC: 2201 AN: 5174

South Asian (SAS) AF: 0.510 AC: 2451 AN: 4810

European-Finnish (FIN) AF: 0.479 AC: 5058 AN: 10558

Middle Eastern (MID) AF: 0.415 AC: 122 AN: 294

European-Non Finnish (NFE) AF: 0.487 AC: 33050 AN: 67898

Other (OTH) AF: 0.375 AC: 788 AN: 2104

Alfa AF: 0.448 Hom.: 26890

Bravo AF: 0.370

Asia WGS AF: 0.430 AC: 1498 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	0.092
DANN	Benign	0.12
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs3810427; hg19: chr19-16046650;