19-54705812-G-A

Variant names:

• chr19-54705812-G-A
• rs12151161

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 0.836 in 152,226 control chromosomes in the GnomAD database, including 53,676 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 0.84 (53676 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0340
• Publications: 5 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.892 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: 0.836 AC: 127137 AN: 152108 Hom.: 53639 Cov.: 32

Gnomad AFR AF: 0.705

Gnomad AMI AF: 0.852

Gnomad AMR AF: 0.817

Gnomad ASJ AF: 0.884

Gnomad EAS AF: 0.839

Gnomad SAS AF: 0.882

Gnomad FIN AF: 0.931

Gnomad MID AF: 0.892

Gnomad NFE AF: 0.898

Gnomad OTH AF: 0.851

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

GnomAD4 genome AF: 0.836 AC: 127232 AN: 152226 Hom.: 53676 Cov.: 32 AF XY: 0.839 AC XY: 62455 AN XY: 74436

African (AFR) AF: 0.706 AC: 29286 AN: 41502

American (AMR) AF: 0.817 AC: 12493 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.884 AC: 3066 AN: 3468

East Asian (EAS) AF: 0.839 AC: 4348 AN: 5184

South Asian (SAS) AF: 0.883 AC: 4254 AN: 4820

European-Finnish (FIN) AF: 0.931 AC: 9876 AN: 10610

Middle Eastern (MID) AF: 0.884 AC: 260 AN: 294

European-Non Finnish (NFE) AF: 0.898 AC: 61072 AN: 68026

Other (OTH) AF: 0.851 AC: 1800 AN: 2114

Alfa AF: 0.852 Hom.: 59314

Bravo AF: 0.822

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	2.4
PhyloP100		0.034

Splicing

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

Other links and lift over

dbSNP: rs12151161; hg19: chr19-55217589;