19-54404500-C-T

Variant names:

• chr19-54404500-C-T
• rs11084337

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 4 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.329 AC: 13541 AN: 41138

American (AMR) AF: 0.543 AC: 8233 AN: 15156

Ashkenazi Jewish (ASJ) AF: 0.608 AC: 2105 AN: 3462

East Asian (EAS) AF: 0.578 AC: 2971 AN: 5138

South Asian (SAS) AF: 0.643 AC: 3084 AN: 4798

European-Finnish (FIN) AF: 0.655 AC: 6758 AN: 10324

Middle Eastern (MID) AF: 0.507 AC: 147 AN: 290

European-Non Finnish (NFE) AF: 0.597 AC: 40530 AN: 67882

Other (OTH) AF: 0.553 AC: 1157 AN: 2092

Alfa AF: 0.569 Hom.: 29626

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
PhyloP100		-1.5

Splicing

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

Other links and lift over

dbSNP: rs11084337; hg19: chr19-54916104;