rs17572584

chr3-143169201-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 0.107 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/exons	MANE	UniProt

Ensembl

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