19-17401603-G-A

Variant names:

• chr19-17401603-G-A
• rs10415893

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 0.18 in 151,124 control chromosomes in the GnomAD database, including 2,645 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 0.18 (2645 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.369
• Publications: 24 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.267 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: 0.180 AC: 27175 AN: 151006 Hom.: 2637 Cov.: 30

Gnomad AFR AF: 0.271

Gnomad AMI AF: 0.0691

Gnomad AMR AF: 0.150

Gnomad ASJ AF: 0.203

Gnomad EAS AF: 0.197

Gnomad SAS AF: 0.261

Gnomad FIN AF: 0.168

Gnomad MID AF: 0.213

Gnomad NFE AF: 0.126

Gnomad OTH AF: 0.197

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

GnomAD4 genome AF: 0.180 AC: 27218 AN: 151124 Hom.: 2645 Cov.: 30 AF XY: 0.184 AC XY: 13525 AN XY: 73694

African (AFR) AF: 0.271 AC: 11136 AN: 41124

American (AMR) AF: 0.150 AC: 2268 AN: 15150

Ashkenazi Jewish (ASJ) AF: 0.203 AC: 705 AN: 3472

East Asian (EAS) AF: 0.197 AC: 1009 AN: 5118

South Asian (SAS) AF: 0.262 AC: 1259 AN: 4800

European-Finnish (FIN) AF: 0.168 AC: 1722 AN: 10266

Middle Eastern (MID) AF: 0.212 AC: 62 AN: 292

European-Non Finnish (NFE) AF: 0.126 AC: 8570 AN: 67898

Other (OTH) AF: 0.203 AC: 424 AN: 2092

Alfa AF: 0.145 Hom.: 7355

Bravo AF: 0.180

Asia WGS AF: 0.238 AC: 826 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.36
DANN	Benign	0.81
PhyloP100		-0.37

Splicing

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

Other links and lift over

dbSNP: rs10415893; hg19: chr19-17512412;