chr19-51458762-C-T

Position:

• chr19-51458762-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 0.863 in 152,158 control chromosomes in the GnomAD database, including 57,063 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 0.86 (57063 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.06

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 (AFR) allele frequency at 95% confidence interval = 0.954 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: 0.863 AC: 131151 AN: 152040 Hom.: 57004 Cov.: 31

Gnomad AFR AF: 0.962

Gnomad AMI AF: 0.822

Gnomad AMR AF: 0.882

Gnomad ASJ AF: 0.868

Gnomad EAS AF: 0.880

Gnomad SAS AF: 0.849

Gnomad FIN AF: 0.770

Gnomad MID AF: 0.861

Gnomad NFE AF: 0.812

Gnomad OTH AF: 0.876

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

GnomAD4 genome AF: 0.863 AC: 131272 AN: 152158 Hom.: 57063 Cov.: 31 AF XY: 0.862 AC XY: 64105 AN XY: 74362

Gnomad4 AFR AF: 0.962

Gnomad4 AMR AF: 0.882

Gnomad4 ASJ AF: 0.868

Gnomad4 EAS AF: 0.879

Gnomad4 SAS AF: 0.848

Gnomad4 FIN AF: 0.770

Gnomad4 NFE AF: 0.812

Gnomad4 OTH AF: 0.874

Alfa AF: 0.829 Hom.: 28342

Bravo AF: 0.876

Asia WGS AF: 0.861 AC: 2995 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	1.2
DANN	Benign	0.20

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs36496; hg19: chr19-51962016;