rs17572584

Variant names:

• chr3-143169201-C-T
• rs17572584

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 0.107 in 152,146 control chromosomes in the GnomAD database, including 939 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 0.11 (939 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.50

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.112 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: 0.107 AC: 16304 AN: 152028 Hom.: 937 Cov.: 32

Gnomad AFR AF: 0.115

Gnomad AMI AF: 0.112

Gnomad AMR AF: 0.0729

Gnomad ASJ AF: 0.0752

Gnomad EAS AF: 0.0270

Gnomad SAS AF: 0.0592

Gnomad FIN AF: 0.155

Gnomad MID AF: 0.127

Gnomad NFE AF: 0.114

Gnomad OTH AF: 0.0997

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

GnomAD4 genome AF: 0.107 AC: 16314 AN: 152146 Hom.: 939 Cov.: 32 AF XY: 0.106 AC XY: 7918 AN XY: 74380

Gnomad4 AFR AF: 0.115

Gnomad4 AMR AF: 0.0727

Gnomad4 ASJ AF: 0.0752

Gnomad4 EAS AF: 0.0271

Gnomad4 SAS AF: 0.0592

Gnomad4 FIN AF: 0.155

Gnomad4 NFE AF: 0.114

Gnomad4 OTH AF: 0.101

Alfa AF: 0.106 Hom.: 1261

Bravo AF: 0.101

Asia WGS AF: 0.0560 AC: 195 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.080
DANN	Benign	0.46

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17572584; hg19: chr3-142888043;