rs4312419

Positions:

• chr19-15716921-G-A
• chr19-15716921-G-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 0.211 in 151,900 control chromosomes in the GnomAD database, including 3,128 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 0.21 (3128 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.14

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.219 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: 0.211 AC: 32039 AN: 151782 Hom.: 3122 Cov.: 31

Gnomad AFR AF: 0.222

Gnomad AMI AF: 0.241

Gnomad AMR AF: 0.152

Gnomad ASJ AF: 0.193

Gnomad EAS AF: 0.128

Gnomad SAS AF: 0.222

Gnomad FIN AF: 0.229

Gnomad MID AF: 0.177

Gnomad NFE AF: 0.222

Gnomad OTH AF: 0.183

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

GnomAD4 genome AF: 0.211 AC: 32070 AN: 151900 Hom.: 3128 Cov.: 31 AF XY: 0.209 AC XY: 15510 AN XY: 74262

Gnomad4 AFR AF: 0.222

Gnomad4 AMR AF: 0.152

Gnomad4 ASJ AF: 0.193

Gnomad4 EAS AF: 0.127

Gnomad4 SAS AF: 0.221

Gnomad4 FIN AF: 0.229

Gnomad4 NFE AF: 0.222

Gnomad4 OTH AF: 0.180

Alfa AF: 0.195 Hom.: 1359

Asia WGS AF: 0.164 AC: 570 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.8
DANN	Benign	0.42

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4312419; hg19: chr19-15827731;