rs12602195

chr17-34333130-A-G

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 0.156 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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.0591

Gnomad4 AMR AF: 0.259

Gnomad4 ASJ AF: 0.164

Gnomad4 EAS AF: 0.293

Gnomad4 SAS AF: 0.375

Gnomad4 FIN AF: 0.150

Gnomad4 NFE AF: 0.165

Gnomad4 OTH AF: 0.172

Alfa AF: 0.173 Hom.: 4606

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12602195; hg19: chr17-32660149;