19-50903362-A-G

Variant names:

• chr19-50903362-A-G
• rs2569531

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 0.451 in 151,750 control chromosomes in the GnomAD database, including 17,255 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 0.45 (17255 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.26
• Publications: 1 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 (AFR) allele frequency at 95% confidence interval = 0.679 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: 0.451 AC: 68320 AN: 151632 Hom.: 17226 Cov.: 30

Gnomad AFR AF: 0.686

Gnomad AMI AF: 0.360

Gnomad AMR AF: 0.383

Gnomad ASJ AF: 0.382

Gnomad EAS AF: 0.174

Gnomad SAS AF: 0.415

Gnomad FIN AF: 0.320

Gnomad MID AF: 0.475

Gnomad NFE AF: 0.371

Gnomad OTH AF: 0.447

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

GnomAD4 genome AF: 0.451 AC: 68399 AN: 151750 Hom.: 17255 Cov.: 30 AF XY: 0.446 AC XY: 33049 AN XY: 74136

African (AFR) AF: 0.686 AC: 28388 AN: 41386

American (AMR) AF: 0.382 AC: 5829 AN: 15242

Ashkenazi Jewish (ASJ) AF: 0.382 AC: 1322 AN: 3458

East Asian (EAS) AF: 0.174 AC: 888 AN: 5108

South Asian (SAS) AF: 0.417 AC: 1995 AN: 4786

European-Finnish (FIN) AF: 0.320 AC: 3380 AN: 10548

Middle Eastern (MID) AF: 0.486 AC: 142 AN: 292

European-Non Finnish (NFE) AF: 0.371 AC: 25196 AN: 67914

Other (OTH) AF: 0.442 AC: 933 AN: 2110

Alfa AF: 0.401 Hom.: 1626

Bravo AF: 0.464

Asia WGS AF: 0.322 AC: 1123 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	1.0
DANN	Benign	0.65
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs2569531; hg19: chr19-51406618;