rs4381710

chr19-15718554-C-T

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;