chr19-50931527-C-T

Variant names:

• chr19-50931527-C-T
• rs17800874

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 0.167 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
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.0545 AC: 2237 AN: 41072

American (AMR) AF: 0.139 AC: 2097 AN: 15138

Ashkenazi Jewish (ASJ) AF: 0.122 AC: 422 AN: 3460

East Asian (EAS) AF: 0.786 AC: 3987 AN: 5072

South Asian (SAS) AF: 0.394 AC: 1876 AN: 4762

European-Finnish (FIN) AF: 0.168 AC: 1729 AN: 10320

Middle Eastern (MID) AF: 0.106 AC: 31 AN: 292

European-Non Finnish (NFE) AF: 0.183 AC: 12393 AN: 67778

Other (OTH) AF: 0.151 AC: 318 AN: 2100

Alfa AF: 0.171 Hom.: 3886

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
PhyloP100		-0.072

Splicing

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

Other links and lift over

dbSNP: rs17800874; hg19: chr19-51434783;