12-18871624-G-A

Variant names:

• chr12-18871624-G-A
• rs12319113

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 0.141 in 152,072 control chromosomes in the GnomAD database, including 2,519 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 0.14 (2519 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.370
• Publications: 1 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 (AFR) allele frequency at 95% confidence interval = 0.32 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: 0.140 AC: 21349 AN: 151954 Hom.: 2512 Cov.: 31

Gnomad AFR AF: 0.325

Gnomad AMI AF: 0.121

Gnomad AMR AF: 0.0774

Gnomad ASJ AF: 0.164

Gnomad EAS AF: 0.0648

Gnomad SAS AF: 0.0505

Gnomad FIN AF: 0.0875

Gnomad MID AF: 0.197

Gnomad NFE AF: 0.0624

Gnomad OTH AF: 0.117

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

GnomAD4 genome AF: 0.141 AC: 21385 AN: 152072 Hom.: 2519 Cov.: 31 AF XY: 0.141 AC XY: 10482 AN XY: 74342

African (AFR) AF: 0.325 AC: 13477 AN: 41482

American (AMR) AF: 0.0771 AC: 1177 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.164 AC: 570 AN: 3472

East Asian (EAS) AF: 0.0643 AC: 331 AN: 5144

South Asian (SAS) AF: 0.0507 AC: 244 AN: 4812

European-Finnish (FIN) AF: 0.0875 AC: 928 AN: 10600

Middle Eastern (MID) AF: 0.205 AC: 60 AN: 292

European-Non Finnish (NFE) AF: 0.0624 AC: 4241 AN: 67990

Other (OTH) AF: 0.117 AC: 247 AN: 2108

Alfa AF: 0.0259 Hom.: 25

Bravo AF: 0.151

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.0
DANN	Benign	0.57
PhyloP100		-0.37

Splicing

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

Other links and lift over

dbSNP: rs12319113; hg19: chr12-19024558;