rs3736328

chr19-18152893-C-Gchr19-18152893-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 0.481 in 152,104 control chromosomes in the GnomAD database, including 18,253 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 0.48 (18253 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.56

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.723 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: 0.482 AC: 73220 AN: 151986 Hom.: 18255 Cov.: 33

Gnomad AFR AF: 0.355

Gnomad AMI AF: 0.714

Gnomad AMR AF: 0.510

Gnomad ASJ AF: 0.477

Gnomad EAS AF: 0.743

Gnomad SAS AF: 0.654

Gnomad FIN AF: 0.482

Gnomad MID AF: 0.503

Gnomad NFE AF: 0.517

Gnomad OTH AF: 0.472

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

GnomAD4 genome AF: 0.481 AC: 73237 AN: 152104 Hom.: 18253 Cov.: 33 AF XY: 0.482 AC XY: 35837 AN XY: 74342

Gnomad4 AFR AF: 0.355

Gnomad4 AMR AF: 0.510

Gnomad4 ASJ AF: 0.477

Gnomad4 EAS AF: 0.742

Gnomad4 SAS AF: 0.654

Gnomad4 FIN AF: 0.482

Gnomad4 NFE AF: 0.517

Gnomad4 OTH AF: 0.476

Alfa AF: 0.487 Hom.: 2264

Bravo AF: 0.475

Asia WGS AF: 0.672 AC: 2334 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
Cadd	Benign	0.030
Dann	Benign	0.44

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3736328; hg19: chr19-18263703;