chr19-15718554-C-T

Variant names:

• chr19-15718554-C-T
• rs4381710

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 0.302 in 151,824 control chromosomes in the GnomAD database, including 7,189 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 0.30 (7189 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.05
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.679 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: 0.301 AC: 45723 AN: 151706 Hom.: 7177 Cov.: 31

Gnomad AFR AF: 0.268

Gnomad AMI AF: 0.305

Gnomad AMR AF: 0.382

Gnomad ASJ AF: 0.244

Gnomad EAS AF: 0.699

Gnomad SAS AF: 0.346

Gnomad FIN AF: 0.306

Gnomad MID AF: 0.206

Gnomad NFE AF: 0.274

Gnomad OTH AF: 0.273

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

GnomAD4 genome AF: 0.302 AC: 45777 AN: 151824 Hom.: 7189 Cov.: 31 AF XY: 0.306 AC XY: 22713 AN XY: 74188

African (AFR) AF: 0.269 AC: 11111 AN: 41354

American (AMR) AF: 0.382 AC: 5829 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.244 AC: 848 AN: 3470

East Asian (EAS) AF: 0.698 AC: 3593 AN: 5144

South Asian (SAS) AF: 0.345 AC: 1657 AN: 4806

European-Finnish (FIN) AF: 0.306 AC: 3211 AN: 10508

Middle Eastern (MID) AF: 0.201 AC: 59 AN: 294

European-Non Finnish (NFE) AF: 0.274 AC: 18613 AN: 67962

Other (OTH) AF: 0.274 AC: 579 AN: 2110

Alfa AF: 0.283 Hom.: 3118

Asia WGS AF: 0.481 AC: 1668 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	2.3
DANN	Benign	0.37
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs4381710; hg19: chr19-15829364;