chr12-114835070-T-C

Variant names:

• chr12-114835070-T-C
• rs2992630

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 0.328 in 152,042 control chromosomes in the GnomAD database, including 9,275 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 0.33 (9275 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.174
• Publications: 3 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 = 0.68 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: 0.328 AC: 49783 AN: 151924 Hom.: 9273 Cov.: 32

Gnomad AFR AF: 0.436

Gnomad AMI AF: 0.344

Gnomad AMR AF: 0.290

Gnomad ASJ AF: 0.281

Gnomad EAS AF: 0.700

Gnomad SAS AF: 0.566

Gnomad FIN AF: 0.227

Gnomad MID AF: 0.394

Gnomad NFE AF: 0.242

Gnomad OTH AF: 0.322

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

GnomAD4 genome AF: 0.328 AC: 49805 AN: 152042 Hom.: 9275 Cov.: 32 AF XY: 0.333 AC XY: 24737 AN XY: 74328

African (AFR) AF: 0.436 AC: 18082 AN: 41468

American (AMR) AF: 0.290 AC: 4427 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.281 AC: 973 AN: 3466

East Asian (EAS) AF: 0.699 AC: 3606 AN: 5156

South Asian (SAS) AF: 0.566 AC: 2725 AN: 4816

European-Finnish (FIN) AF: 0.227 AC: 2400 AN: 10570

Middle Eastern (MID) AF: 0.379 AC: 110 AN: 290

European-Non Finnish (NFE) AF: 0.242 AC: 16481 AN: 67972

Other (OTH) AF: 0.325 AC: 687 AN: 2112

Alfa AF: 0.265 Hom.: 9422

Bravo AF: 0.338

Asia WGS AF: 0.547 AC: 1898 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.5
DANN	Benign	0.48
PhyloP100		-0.17

Splicing

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

Other links and lift over

dbSNP: rs2992630; hg19: chr12-115272875;