rs4381710

Variant names:

• chr19-15718554-C-T
• rs4381710

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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

Gnomad4 AFR AF: 0.269

Gnomad4 AMR AF: 0.382

Gnomad4 ASJ AF: 0.244

Gnomad4 EAS AF: 0.698

Gnomad4 SAS AF: 0.345

Gnomad4 FIN AF: 0.306

Gnomad4 NFE AF: 0.274

Gnomad4 OTH AF: 0.274

Alfa AF: 0.283 Hom.: 2810

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4381710; hg19: chr19-15829364;