chr19-54404500-C-T

Position:

• chr19-54404500-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 0.523 in 151,190 control chromosomes in the GnomAD database, including 21,714 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 0.52 (21714 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.48

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.624 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: 0.523 AC: 79073 AN: 151102 Hom.: 21716 Cov.: 30

Gnomad AFR AF: 0.329

Gnomad AMI AF: 0.616

Gnomad AMR AF: 0.543

Gnomad ASJ AF: 0.608

Gnomad EAS AF: 0.577

Gnomad SAS AF: 0.644

Gnomad FIN AF: 0.655

Gnomad MID AF: 0.500

Gnomad NFE AF: 0.597

Gnomad OTH AF: 0.555

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

GnomAD4 genome AF: 0.523 AC: 79087 AN: 151190 Hom.: 21714 Cov.: 30 AF XY: 0.531 AC XY: 39150 AN XY: 73746

Gnomad4 AFR AF: 0.329

Gnomad4 AMR AF: 0.543

Gnomad4 ASJ AF: 0.608

Gnomad4 EAS AF: 0.578

Gnomad4 SAS AF: 0.643

Gnomad4 FIN AF: 0.655

Gnomad4 NFE AF: 0.597

Gnomad4 OTH AF: 0.553

Alfa AF: 0.587 Hom.: 18873

Bravo AF: 0.504

Asia WGS AF: 0.617 AC: 2149 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	0.47
DANN	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11084337; hg19: chr19-54916104;