rs17530508

Variant names:

• chr19-33369952-C-T
• rs17530508

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 0.12 in 152,188 control chromosomes in the GnomAD database, including 1,448 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 0.12 (1448 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.02
• Publications: 14 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.198 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: 0.120 AC: 18222 AN: 152070 Hom.: 1447 Cov.: 32

Gnomad AFR AF: 0.0289

Gnomad AMI AF: 0.0822

Gnomad AMR AF: 0.0775

Gnomad ASJ AF: 0.145

Gnomad EAS AF: 0.208

Gnomad SAS AF: 0.110

Gnomad FIN AF: 0.184

Gnomad MID AF: 0.136

Gnomad NFE AF: 0.168

Gnomad OTH AF: 0.116

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

GnomAD4 genome AF: 0.120 AC: 18215 AN: 152188 Hom.: 1448 Cov.: 32 AF XY: 0.119 AC XY: 8827 AN XY: 74384

African (AFR) AF: 0.0289 AC: 1199 AN: 41554

American (AMR) AF: 0.0774 AC: 1184 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.145 AC: 503 AN: 3472

East Asian (EAS) AF: 0.208 AC: 1077 AN: 5180

South Asian (SAS) AF: 0.109 AC: 526 AN: 4832

European-Finnish (FIN) AF: 0.184 AC: 1937 AN: 10554

Middle Eastern (MID) AF: 0.143 AC: 42 AN: 294

European-Non Finnish (NFE) AF: 0.168 AC: 11428 AN: 67988

Other (OTH) AF: 0.115 AC: 244 AN: 2114

Alfa AF: 0.155 Hom.: 1818

Bravo AF: 0.108

Asia WGS AF: 0.154 AC: 534 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.16
DANN	Benign	0.22
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs17530508; hg19: chr19-33860858;