rs17800874

Variant names:

• chr19-50931527-C-T
• rs17800874

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.167 in 150,900 control chromosomes in the GnomAD database, including 3,598 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 0.17 (3598 hom., cov: 28)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0720

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.766 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: 0.167 AC: 25224 AN: 150804 Hom.: 3603 Cov.: 28

Gnomad AFR AF: 0.0546

Gnomad AMI AF: 0.142

Gnomad AMR AF: 0.138

Gnomad ASJ AF: 0.122

Gnomad EAS AF: 0.787

Gnomad SAS AF: 0.395

Gnomad FIN AF: 0.168

Gnomad MID AF: 0.102

Gnomad NFE AF: 0.183

Gnomad OTH AF: 0.147

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

GnomAD4 genome AF: 0.167 AC: 25219 AN: 150900 Hom.: 3598 Cov.: 28 AF XY: 0.172 AC XY: 12670 AN XY: 73686

Gnomad4 AFR AF: 0.0545

Gnomad4 AMR AF: 0.139

Gnomad4 ASJ AF: 0.122

Gnomad4 EAS AF: 0.786

Gnomad4 SAS AF: 0.394

Gnomad4 FIN AF: 0.168

Gnomad4 NFE AF: 0.183

Gnomad4 OTH AF: 0.151

Alfa AF: 0.168 Hom.: 2177

Bravo AF: 0.159

Asia WGS AF: 0.538 AC: 1868 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.62
DANN	Benign	0.17

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17800874; hg19: chr19-51434783;