rs3810427

Positions:

• chr19-15935840-C-A

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 0.385 in 151,940 control chromosomes in the GnomAD database, including 12,767 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 0.38 (12767 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.19

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.08).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.493 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.385 AC: 58489 AN: 151822 Hom.: 12771 Cov.: 31

Gnomad AFR AF: 0.161

Gnomad AMI AF: 0.560

Gnomad AMR AF: 0.406

Gnomad ASJ AF: 0.421

Gnomad EAS AF: 0.425

Gnomad SAS AF: 0.510

Gnomad FIN AF: 0.479

Gnomad MID AF: 0.405

Gnomad NFE AF: 0.487

Gnomad OTH AF: 0.375

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

GnomAD4 genome AF: 0.385 AC: 58495 AN: 151940 Hom.: 12767 Cov.: 31 AF XY: 0.384 AC XY: 28546 AN XY: 74268

Gnomad4 AFR AF: 0.161

Gnomad4 AMR AF: 0.406

Gnomad4 ASJ AF: 0.421

Gnomad4 EAS AF: 0.425

Gnomad4 SAS AF: 0.510

Gnomad4 FIN AF: 0.479

Gnomad4 NFE AF: 0.487

Gnomad4 OTH AF: 0.375

Alfa AF: 0.417 Hom.: 1365

Bravo AF: 0.370

Asia WGS AF: 0.430 AC: 1498 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.092
DANN	Benign	0.12

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3810427; hg19: chr19-16046650;