chr19-1175397-A-G

Variant names:

• chr19-1175397-A-G
• rs873289

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 0.473 in 151,882 control chromosomes in the GnomAD database, including 17,194 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 0.47 (17194 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0450
• Publications: 18 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.576 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: 0.473 AC: 71771 AN: 151762 Hom.: 17172 Cov.: 31

Gnomad AFR AF: 0.420

Gnomad AMI AF: 0.617

Gnomad AMR AF: 0.458

Gnomad ASJ AF: 0.487

Gnomad EAS AF: 0.523

Gnomad SAS AF: 0.593

Gnomad FIN AF: 0.548

Gnomad MID AF: 0.506

Gnomad NFE AF: 0.481

Gnomad OTH AF: 0.485

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

GnomAD4 genome AF: 0.473 AC: 71828 AN: 151882 Hom.: 17194 Cov.: 31 AF XY: 0.480 AC XY: 35620 AN XY: 74230

African (AFR) AF: 0.420 AC: 17379 AN: 41416

American (AMR) AF: 0.458 AC: 6997 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.487 AC: 1691 AN: 3470

East Asian (EAS) AF: 0.523 AC: 2698 AN: 5156

South Asian (SAS) AF: 0.594 AC: 2861 AN: 4816

European-Finnish (FIN) AF: 0.548 AC: 5778 AN: 10536

Middle Eastern (MID) AF: 0.507 AC: 149 AN: 294

European-Non Finnish (NFE) AF: 0.481 AC: 32683 AN: 67914

Other (OTH) AF: 0.490 AC: 1032 AN: 2104

Alfa AF: 0.481 Hom.: 14472

Bravo AF: 0.458

Asia WGS AF: 0.593 AC: 2065 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	3.5
DANN	Benign	0.72
PhyloP100		0.045

Splicing

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

Other links and lift over

dbSNP: rs873289; hg19: chr19-1175396;