12-130170530-A-C

Variant names:

• chr12-130170530-A-C
• rs2078105

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 0.101 in 152,274 control chromosomes in the GnomAD database, including 1,100 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 0.10 (1100 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.47
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.242 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.101 AC: 15361 AN: 152156 Hom.: 1099 Cov.: 32

Gnomad AFR AF: 0.0224

Gnomad AMI AF: 0.105

Gnomad AMR AF: 0.134

Gnomad ASJ AF: 0.0890

Gnomad EAS AF: 0.253

Gnomad SAS AF: 0.163

Gnomad FIN AF: 0.172

Gnomad MID AF: 0.123

Gnomad NFE AF: 0.115

Gnomad OTH AF: 0.105

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

GnomAD4 genome AF: 0.101 AC: 15374 AN: 152274 Hom.: 1100 Cov.: 32 AF XY: 0.107 AC XY: 7958 AN XY: 74450

African (AFR) AF: 0.0223 AC: 927 AN: 41574

American (AMR) AF: 0.133 AC: 2041 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.0890 AC: 309 AN: 3472

East Asian (EAS) AF: 0.253 AC: 1311 AN: 5174

South Asian (SAS) AF: 0.164 AC: 792 AN: 4822

European-Finnish (FIN) AF: 0.172 AC: 1823 AN: 10596

Middle Eastern (MID) AF: 0.129 AC: 38 AN: 294

European-Non Finnish (NFE) AF: 0.115 AC: 7806 AN: 68026

Other (OTH) AF: 0.109 AC: 231 AN: 2114

Alfa AF: 0.107 Hom.: 1872

Bravo AF: 0.0943

Asia WGS AF: 0.208 AC: 724 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.20
DANN	Benign	0.50
PhyloP100		-1.5

Splicing

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

Other links and lift over

dbSNP: rs2078105; hg19: chr12-130655075;