12-13996137-G-C

Variant names:

• chr12-13996137-G-C
• rs9300244

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 0.301 in 152,022 control chromosomes in the GnomAD database, including 8,484 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 0.30 (8484 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.38
• Publications: 0 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 = 0.583 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: 0.301 AC: 45772 AN: 151904 Hom.: 8490 Cov.: 33

Gnomad AFR AF: 0.0960

Gnomad AMI AF: 0.300

Gnomad AMR AF: 0.453

Gnomad ASJ AF: 0.392

Gnomad EAS AF: 0.601

Gnomad SAS AF: 0.510

Gnomad FIN AF: 0.332

Gnomad MID AF: 0.459

Gnomad NFE AF: 0.344

Gnomad OTH AF: 0.326

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

GnomAD4 genome AF: 0.301 AC: 45771 AN: 152022 Hom.: 8484 Cov.: 33 AF XY: 0.307 AC XY: 22786 AN XY: 74322

African (AFR) AF: 0.0958 AC: 3975 AN: 41494

American (AMR) AF: 0.453 AC: 6924 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.392 AC: 1361 AN: 3472

East Asian (EAS) AF: 0.600 AC: 3103 AN: 5170

South Asian (SAS) AF: 0.509 AC: 2454 AN: 4818

European-Finnish (FIN) AF: 0.332 AC: 3499 AN: 10538

Middle Eastern (MID) AF: 0.455 AC: 133 AN: 292

European-Non Finnish (NFE) AF: 0.344 AC: 23360 AN: 67950

Other (OTH) AF: 0.327 AC: 689 AN: 2110

Alfa AF: 0.317 Hom.: 1076

Bravo AF: 0.300

Asia WGS AF: 0.520 AC: 1811 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	0.091
DANN	Benign	0.49
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs9300244; hg19: chr12-14149071;