19-48952744-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 0.46 in 152,018 control chromosomes in the GnomAD database, including 17,199 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 0.46 (17199 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.28

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.597 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: 0.460 AC: 69879 AN: 151900 Hom.: 17185 Cov.: 32

Gnomad AFR AF: 0.264

Gnomad AMI AF: 0.489

Gnomad AMR AF: 0.489

Gnomad ASJ AF: 0.498

Gnomad EAS AF: 0.614

Gnomad SAS AF: 0.537

Gnomad FIN AF: 0.578

Gnomad MID AF: 0.484

Gnomad NFE AF: 0.534

Gnomad OTH AF: 0.486

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

GnomAD4 genome AF: 0.460 AC: 69928 AN: 152018 Hom.: 17199 Cov.: 32 AF XY: 0.466 AC XY: 34608 AN XY: 74296

Gnomad4 AFR AF: 0.264

Gnomad4 AMR AF: 0.489

Gnomad4 ASJ AF: 0.498

Gnomad4 EAS AF: 0.614

Gnomad4 SAS AF: 0.539

Gnomad4 FIN AF: 0.578

Gnomad4 NFE AF: 0.534

Gnomad4 OTH AF: 0.486

Alfa AF: 0.521 Hom.: 26341

Bravo AF: 0.446

Asia WGS AF: 0.535 AC: 1859 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
Cadd	Benign	0.31
Dann	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11667229; hg19: chr19-49456001;