19-51461312-A-T

Position:

• chr19-51461312-A-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 0.144 in 152,062 control chromosomes in the GnomAD database, including 2,017 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 0.14 (2017 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.01

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.257 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: 0.143 AC: 21778 AN: 151944 Hom.: 2007 Cov.: 32

Gnomad AFR AF: 0.261

Gnomad AMI AF: 0.0943

Gnomad AMR AF: 0.145

Gnomad ASJ AF: 0.102

Gnomad EAS AF: 0.136

Gnomad SAS AF: 0.0812

Gnomad FIN AF: 0.139

Gnomad MID AF: 0.130

Gnomad NFE AF: 0.0802

Gnomad OTH AF: 0.146

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

GnomAD4 genome AF: 0.144 AC: 21822 AN: 152062 Hom.: 2017 Cov.: 32 AF XY: 0.144 AC XY: 10728 AN XY: 74330

Gnomad4 AFR AF: 0.261

Gnomad4 AMR AF: 0.145

Gnomad4 ASJ AF: 0.102

Gnomad4 EAS AF: 0.136

Gnomad4 SAS AF: 0.0813

Gnomad4 FIN AF: 0.139

Gnomad4 NFE AF: 0.0802

Gnomad4 OTH AF: 0.150

Alfa AF: 0.114 Hom.: 152

Bravo AF: 0.150

Asia WGS AF: 0.167 AC: 580 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	1.3
DANN	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10420357; hg19: chr19-51964566;