rs17143152

Variant names:

• chr7-20598532-G-A
• rs17143152

Your query was ambiguous. Multiple possible variants found:

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

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 0.133 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
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.144 AC: 5962 AN: 41476

American (AMR) AF: 0.0674 AC: 1030 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.122 AC: 424 AN: 3470

East Asian (EAS) AF: 0.289 AC: 1490 AN: 5160

South Asian (SAS) AF: 0.118 AC: 569 AN: 4818

European-Finnish (FIN) AF: 0.225 AC: 2378 AN: 10572

Middle Eastern (MID) AF: 0.0476 AC: 14 AN: 294

European-Non Finnish (NFE) AF: 0.117 AC: 7979 AN: 68012

Other (OTH) AF: 0.110 AC: 233 AN: 2114

Alfa AF: 0.116 Hom.: 2059

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
PhyloP100		0.14

Splicing

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

Other links and lift over

dbSNP: rs17143152; hg19: chr7-20638155;