rs13345980

Variant names:

• chr19-50915604-G-A
• rs13345980

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 0.0622 in 152,092 control chromosomes in the GnomAD database, including 400 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 0.062 (400 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.751
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.12 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: 0.0621 AC: 9441 AN: 151974 Hom.: 398 Cov.: 32

Gnomad AFR AF: 0.123

Gnomad AMI AF: 0.00548

Gnomad AMR AF: 0.0372

Gnomad ASJ AF: 0.0159

Gnomad EAS AF: 0.000193

Gnomad SAS AF: 0.0430

Gnomad FIN AF: 0.0302

Gnomad MID AF: 0.0190

Gnomad NFE AF: 0.0456

Gnomad OTH AF: 0.0488

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

GnomAD4 genome AF: 0.0622 AC: 9456 AN: 152092 Hom.: 400 Cov.: 32 AF XY: 0.0607 AC XY: 4517 AN XY: 74372

African (AFR) AF: 0.123 AC: 5097 AN: 41448

American (AMR) AF: 0.0372 AC: 568 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.0159 AC: 55 AN: 3466

East Asian (EAS) AF: 0.000193 AC: 1 AN: 5174

South Asian (SAS) AF: 0.0426 AC: 205 AN: 4810

European-Finnish (FIN) AF: 0.0302 AC: 320 AN: 10604

Middle Eastern (MID) AF: 0.0204 AC: 6 AN: 294

European-Non Finnish (NFE) AF: 0.0455 AC: 3096 AN: 67994

Other (OTH) AF: 0.0487 AC: 103 AN: 2114

Alfa AF: 0.0483 Hom.: 333

Bravo AF: 0.0648

Asia WGS AF: 0.0210 AC: 74 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	4.2
DANN	Benign	0.71
PhyloP100		-0.75

Splicing

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

Other links and lift over

dbSNP: rs13345980; hg19: chr19-51418860;