19-50902873-A-G

Variant names:

• chr19-50902873-A-G
• rs11881354

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 0.348 in 141,996 control chromosomes in the GnomAD database, including 8,870 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 0.35 (8870 hom., cov: 23)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.140
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.403 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: 0.348 AC: 49374 AN: 141888 Hom.: 8859 Cov.: 23

Gnomad AFR AF: 0.351

Gnomad AMI AF: 0.347

Gnomad AMR AF: 0.331

Gnomad ASJ AF: 0.329

Gnomad EAS AF: 0.169

Gnomad SAS AF: 0.418

Gnomad FIN AF: 0.315

Gnomad MID AF: 0.449

Gnomad NFE AF: 0.363

Gnomad OTH AF: 0.366

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

GnomAD4 genome AF: 0.348 AC: 49411 AN: 141996 Hom.: 8870 Cov.: 23 AF XY: 0.346 AC XY: 23689 AN XY: 68474

African (AFR) AF: 0.351 AC: 13350 AN: 38026

American (AMR) AF: 0.330 AC: 4437 AN: 13436

Ashkenazi Jewish (ASJ) AF: 0.329 AC: 1104 AN: 3354

East Asian (EAS) AF: 0.169 AC: 829 AN: 4912

South Asian (SAS) AF: 0.419 AC: 1839 AN: 4388

European-Finnish (FIN) AF: 0.315 AC: 2799 AN: 8878

Middle Eastern (MID) AF: 0.456 AC: 123 AN: 270

European-Non Finnish (NFE) AF: 0.363 AC: 23920 AN: 65900

Other (OTH) AF: 0.361 AC: 710 AN: 1968

Alfa AF: 0.343 Hom.: 1155

Bravo AF: 0.351

Asia WGS AF: 0.291 AC: 983 AN: 3376

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	4.0
DANN	Benign	0.37
PhyloP100		0.14

Splicing

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

Other links and lift over

dbSNP: rs11881354; hg19: chr19-51406129;