rs12602195

Variant names:

• chr17-34333130-A-G
• rs12602195

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 0.156 in 152,226 control chromosomes in the GnomAD database, including 2,404 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 0.16 (2404 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.290
• Publications: 14 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.361 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: 0.156 AC: 23680 AN: 152106 Hom.: 2395 Cov.: 32

Gnomad AFR AF: 0.0590

Gnomad AMI AF: 0.167

Gnomad AMR AF: 0.258

Gnomad ASJ AF: 0.164

Gnomad EAS AF: 0.294

Gnomad SAS AF: 0.375

Gnomad FIN AF: 0.150

Gnomad MID AF: 0.162

Gnomad NFE AF: 0.165

Gnomad OTH AF: 0.166

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

GnomAD4 genome AF: 0.156 AC: 23718 AN: 152226 Hom.: 2404 Cov.: 32 AF XY: 0.162 AC XY: 12047 AN XY: 74422

African (AFR) AF: 0.0591 AC: 2457 AN: 41562

American (AMR) AF: 0.259 AC: 3959 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.164 AC: 570 AN: 3468

East Asian (EAS) AF: 0.293 AC: 1518 AN: 5176

South Asian (SAS) AF: 0.375 AC: 1807 AN: 4820

European-Finnish (FIN) AF: 0.150 AC: 1593 AN: 10604

Middle Eastern (MID) AF: 0.168 AC: 49 AN: 292

European-Non Finnish (NFE) AF: 0.165 AC: 11248 AN: 67988

Other (OTH) AF: 0.172 AC: 365 AN: 2116

Alfa AF: 0.169 Hom.: 8787

Bravo AF: 0.157

Asia WGS AF: 0.304 AC: 1053 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	6.1
DANN	Benign	0.84
PhyloP100		0.29

Splicing

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

Other links and lift over

dbSNP: rs12602195; hg19: chr17-32660149;