12-13388490-C-G

Variant names:

• chr12-13388490-C-G
• rs1457623

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 0.107 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
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.0511 AC: 2124 AN: 41532

American (AMR) AF: 0.0826 AC: 1264 AN: 15306

Ashkenazi Jewish (ASJ) AF: 0.108 AC: 375 AN: 3472

East Asian (EAS) AF: 0.0822 AC: 426 AN: 5184

South Asian (SAS) AF: 0.110 AC: 531 AN: 4820

European-Finnish (FIN) AF: 0.117 AC: 1243 AN: 10588

Middle Eastern (MID) AF: 0.134 AC: 39 AN: 292

European-Non Finnish (NFE) AF: 0.146 AC: 9927 AN: 68030

Other (OTH) AF: 0.104 AC: 220 AN: 2114

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	0.78
DANN	Benign	0.85
PhyloP100		-0.34

Splicing

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

Other links and lift over

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