19-54404500-C-T

Variant names:

• chr19-54404500-C-T
• rs11084337

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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;