rs17800874

chr19-50931527-C-T

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;