12-114236456-T-C

Variant names:

• chr12-114236456-T-C
• rs2701108

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 0.347 in 151,940 control chromosomes in the GnomAD database, including 9,526 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 0.35 (9526 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.290
• Publications: 16 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.408 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: 0.348 AC: 52778 AN: 151822 Hom.: 9523 Cov.: 31

Gnomad AFR AF: 0.279

Gnomad AMI AF: 0.554

Gnomad AMR AF: 0.344

Gnomad ASJ AF: 0.399

Gnomad EAS AF: 0.185

Gnomad SAS AF: 0.423

Gnomad FIN AF: 0.331

Gnomad MID AF: 0.361

Gnomad NFE AF: 0.395

Gnomad OTH AF: 0.330

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

GnomAD4 genome AF: 0.347 AC: 52798 AN: 151940 Hom.: 9526 Cov.: 31 AF XY: 0.345 AC XY: 25585 AN XY: 74250

African (AFR) AF: 0.278 AC: 11538 AN: 41432

American (AMR) AF: 0.344 AC: 5248 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.399 AC: 1383 AN: 3466

East Asian (EAS) AF: 0.185 AC: 950 AN: 5142

South Asian (SAS) AF: 0.423 AC: 2034 AN: 4808

European-Finnish (FIN) AF: 0.331 AC: 3492 AN: 10558

Middle Eastern (MID) AF: 0.361 AC: 106 AN: 294

European-Non Finnish (NFE) AF: 0.395 AC: 26842 AN: 67942

Other (OTH) AF: 0.332 AC: 700 AN: 2108

Alfa AF: 0.378 Hom.: 46372

Bravo AF: 0.341

Asia WGS AF: 0.292 AC: 1016 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	3.8
DANN	Benign	0.45
PhyloP100		0.29

Splicing

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

Other links and lift over

dbSNP: rs2701108; hg19: chr12-114674261;