19-51724663-C-T

Position:

• chr19-51724663-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 0.752 in 151,838 control chromosomes in the GnomAD database, including 43,238 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 0.75 (43238 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.299

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.967 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: 0.752 AC: 114078 AN: 151720 Hom.: 43184 Cov.: 30

Gnomad AFR AF: 0.739

Gnomad AMI AF: 0.536

Gnomad AMR AF: 0.796

Gnomad ASJ AF: 0.662

Gnomad EAS AF: 0.990

Gnomad SAS AF: 0.833

Gnomad FIN AF: 0.796

Gnomad MID AF: 0.687

Gnomad NFE AF: 0.727

Gnomad OTH AF: 0.735

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

GnomAD4 genome AF: 0.752 AC: 114186 AN: 151838 Hom.: 43238 Cov.: 30 AF XY: 0.757 AC XY: 56134 AN XY: 74170

Gnomad4 AFR AF: 0.739

Gnomad4 AMR AF: 0.797

Gnomad4 ASJ AF: 0.662

Gnomad4 EAS AF: 0.990

Gnomad4 SAS AF: 0.833

Gnomad4 FIN AF: 0.796

Gnomad4 NFE AF: 0.727

Gnomad4 OTH AF: 0.739

Alfa AF: 0.733 Hom.: 55662

Bravo AF: 0.751

Asia WGS AF: 0.913 AC: 3170 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	6.7
DANN	Benign	0.93

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11672222; hg19: chr19-52227916; COSMIC: COSV55786336;