rs17143152

Positions:

• chr7-20598532-G-A
• chr7-20598532-G-C

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 0.133 in 152,106 control chromosomes in the GnomAD database, including 1,518 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 0.13 (1518 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.145

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.277 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: 0.133 AC: 20246 AN: 151988 Hom.: 1523 Cov.: 32

Gnomad AFR AF: 0.144

Gnomad AMI AF: 0.186

Gnomad AMR AF: 0.0676

Gnomad ASJ AF: 0.122

Gnomad EAS AF: 0.289

Gnomad SAS AF: 0.118

Gnomad FIN AF: 0.225

Gnomad MID AF: 0.0411

Gnomad NFE AF: 0.117

Gnomad OTH AF: 0.109

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

GnomAD4 genome AF: 0.133 AC: 20248 AN: 152106 Hom.: 1518 Cov.: 32 AF XY: 0.136 AC XY: 10131 AN XY: 74342

Gnomad4 AFR AF: 0.144

Gnomad4 AMR AF: 0.0674

Gnomad4 ASJ AF: 0.122

Gnomad4 EAS AF: 0.289

Gnomad4 SAS AF: 0.118

Gnomad4 FIN AF: 0.225

Gnomad4 NFE AF: 0.117

Gnomad4 OTH AF: 0.110

Alfa AF: 0.0855 Hom.: 219

Bravo AF: 0.122

Asia WGS AF: 0.198 AC: 689 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	3.4
DANN	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17143152; hg19: chr7-20638155;