chr12-120938613-C-T

Variant names:

• chr12-120938613-C-T
• rs1186380

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 0.389 in 151,902 control chromosomes in the GnomAD database, including 15,066 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 0.39 (15066 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.47

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.726 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: 0.389 AC: 58975 AN: 151784 Hom.: 15029 Cov.: 31

Gnomad AFR AF: 0.733

Gnomad AMI AF: 0.268

Gnomad AMR AF: 0.254

Gnomad ASJ AF: 0.217

Gnomad EAS AF: 0.401

Gnomad SAS AF: 0.359

Gnomad FIN AF: 0.195

Gnomad MID AF: 0.207

Gnomad NFE AF: 0.253

Gnomad OTH AF: 0.326

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

GnomAD4 genome AF: 0.389 AC: 59068 AN: 151902 Hom.: 15066 Cov.: 31 AF XY: 0.383 AC XY: 28430 AN XY: 74246

Gnomad4 AFR AF: 0.733

Gnomad4 AMR AF: 0.255

Gnomad4 ASJ AF: 0.217

Gnomad4 EAS AF: 0.401

Gnomad4 SAS AF: 0.359

Gnomad4 FIN AF: 0.195

Gnomad4 NFE AF: 0.253

Gnomad4 OTH AF: 0.324

Alfa AF: 0.292 Hom.: 4096

Bravo AF: 0.409

Asia WGS AF: 0.378 AC: 1314 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.2
DANN	Benign	0.52

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1186380; hg19: chr12-121376416;