12-114908619-C-T

Variant names:

• chr12-114908619-C-T
• rs1896312

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The variant allele was found at a frequency of 0.708 in 151,884 control chromosomes in the GnomAD database, including 38,565 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 0.71 (38565 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.99
• Publications: 32 publications found

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.37).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.751 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: 0.708 AC: 107508 AN: 151766 Hom.: 38530 Cov.: 30

Gnomad AFR AF: 0.758

Gnomad AMI AF: 0.843

Gnomad AMR AF: 0.579

Gnomad ASJ AF: 0.861

Gnomad EAS AF: 0.472

Gnomad SAS AF: 0.721

Gnomad FIN AF: 0.684

Gnomad MID AF: 0.832

Gnomad NFE AF: 0.718

Gnomad OTH AF: 0.709

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

GnomAD4 genome AF: 0.708 AC: 107600 AN: 151884 Hom.: 38565 Cov.: 30 AF XY: 0.702 AC XY: 52055 AN XY: 74180

African (AFR) AF: 0.758 AC: 31397 AN: 41412

American (AMR) AF: 0.578 AC: 8823 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.861 AC: 2986 AN: 3468

East Asian (EAS) AF: 0.473 AC: 2428 AN: 5138

South Asian (SAS) AF: 0.721 AC: 3466 AN: 4806

European-Finnish (FIN) AF: 0.684 AC: 7207 AN: 10538

Middle Eastern (MID) AF: 0.833 AC: 245 AN: 294

European-Non Finnish (NFE) AF: 0.718 AC: 48784 AN: 67952

Other (OTH) AF: 0.709 AC: 1497 AN: 2110

Alfa AF: 0.710 Hom.: 120099

Bravo AF: 0.701

Asia WGS AF: 0.635 AC: 2212 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.37
CADD	Benign	18
DANN	Benign	0.60
PhyloP100		2.0

Splicing

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

Other links and lift over

dbSNP: rs1896312; hg19: chr12-115346424;