12-13388490-C-G

Variant names:

• chr12-13388490-C-G
• rs1457623

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 0.107 in 152,250 control chromosomes in the GnomAD database, including 980 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 0.11 (980 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.345

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.144 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: 0.107 AC: 16223 AN: 152132 Hom.: 981 Cov.: 33

Gnomad AFR AF: 0.0511

Gnomad AMI AF: 0.0822

Gnomad AMR AF: 0.0827

Gnomad ASJ AF: 0.108

Gnomad EAS AF: 0.0820

Gnomad SAS AF: 0.111

Gnomad FIN AF: 0.117

Gnomad MID AF: 0.131

Gnomad NFE AF: 0.146

Gnomad OTH AF: 0.105

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

GnomAD4 genome AF: 0.107 AC: 16224 AN: 152250 Hom.: 980 Cov.: 33 AF XY: 0.106 AC XY: 7870 AN XY: 74428

Gnomad4 AFR AF: 0.0511

Gnomad4 AMR AF: 0.0826

Gnomad4 ASJ AF: 0.108

Gnomad4 EAS AF: 0.0822

Gnomad4 SAS AF: 0.110

Gnomad4 FIN AF: 0.117

Gnomad4 NFE AF: 0.146

Gnomad4 OTH AF: 0.104

Alfa AF: 0.130 Hom.: 176

Bravo AF: 0.0999

Asia WGS AF: 0.0810 AC: 286 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	0.78
DANN	Benign	0.85

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1457623; hg19: chr12-13541424; COSMIC: COSV73244107;