rs3794987

Variant names:

• chr19-15640081-A-G
• rs3794987

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 0.456 in 151,860 control chromosomes in the GnomAD database, including 16,614 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 0.46 (16614 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.940
• Publications: 12 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.527 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: 0.456 AC: 69246 AN: 151742 Hom.: 16606 Cov.: 30

Gnomad AFR AF: 0.356

Gnomad AMI AF: 0.503

Gnomad AMR AF: 0.437

Gnomad ASJ AF: 0.488

Gnomad EAS AF: 0.205

Gnomad SAS AF: 0.384

Gnomad FIN AF: 0.531

Gnomad MID AF: 0.449

Gnomad NFE AF: 0.531

Gnomad OTH AF: 0.479

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

GnomAD4 genome AF: 0.456 AC: 69285 AN: 151860 Hom.: 16614 Cov.: 30 AF XY: 0.452 AC XY: 33567 AN XY: 74220

African (AFR) AF: 0.356 AC: 14746 AN: 41384

American (AMR) AF: 0.437 AC: 6669 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.488 AC: 1692 AN: 3470

East Asian (EAS) AF: 0.205 AC: 1061 AN: 5166

South Asian (SAS) AF: 0.385 AC: 1846 AN: 4796

European-Finnish (FIN) AF: 0.531 AC: 5605 AN: 10560

Middle Eastern (MID) AF: 0.449 AC: 132 AN: 294

European-Non Finnish (NFE) AF: 0.531 AC: 36080 AN: 67910

Other (OTH) AF: 0.473 AC: 996 AN: 2104

Alfa AF: 0.506 Hom.: 23295

Bravo AF: 0.446

Asia WGS AF: 0.309 AC: 1078 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.78
DANN	Benign	0.45
PhyloP100		-0.94

Splicing

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

Other links and lift over

dbSNP: rs3794987; hg19: chr19-15750891;