rs12970134

Variant names:

• chr18-60217517-G-A
• rs12970134

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 0.213 in 152,116 control chromosomes in the GnomAD database, including 3,812 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 0.21 (3812 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.363

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.33 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: 0.213 AC: 32430 AN: 151998 Hom.: 3810 Cov.: 32

Gnomad AFR AF: 0.140

Gnomad AMI AF: 0.338

Gnomad AMR AF: 0.172

Gnomad ASJ AF: 0.217

Gnomad EAS AF: 0.170

Gnomad SAS AF: 0.342

Gnomad FIN AF: 0.183

Gnomad MID AF: 0.269

Gnomad NFE AF: 0.264

Gnomad OTH AF: 0.220

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

GnomAD4 genome AF: 0.213 AC: 32435 AN: 152116 Hom.: 3812 Cov.: 32 AF XY: 0.210 AC XY: 15586 AN XY: 74354

Gnomad4 AFR AF: 0.139

Gnomad4 AMR AF: 0.171

Gnomad4 ASJ AF: 0.217

Gnomad4 EAS AF: 0.170

Gnomad4 SAS AF: 0.344

Gnomad4 FIN AF: 0.183

Gnomad4 NFE AF: 0.264

Gnomad4 OTH AF: 0.221

Alfa AF: 0.253 Hom.: 11865

Bravo AF: 0.208

Asia WGS AF: 0.205 AC: 715 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.42
DANN	Benign	0.54

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12970134; hg19: chr18-57884750;