chr12-120933430-C-T

Variant names:

• chr12-120933430-C-T
• rs868795

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 0.245 in 152,010 control chromosomes in the GnomAD database, including 4,992 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 0.24 (4992 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.22
• Publications: 8 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.389 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: 0.245 AC: 37180 AN: 151892 Hom.: 4984 Cov.: 31

Gnomad AFR AF: 0.331

Gnomad AMI AF: 0.237

Gnomad AMR AF: 0.198

Gnomad ASJ AF: 0.160

Gnomad EAS AF: 0.404

Gnomad SAS AF: 0.294

Gnomad FIN AF: 0.182

Gnomad MID AF: 0.161

Gnomad NFE AF: 0.202

Gnomad OTH AF: 0.216

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

GnomAD4 genome AF: 0.245 AC: 37221 AN: 152010 Hom.: 4992 Cov.: 31 AF XY: 0.246 AC XY: 18267 AN XY: 74300

African (AFR) AF: 0.331 AC: 13731 AN: 41440

American (AMR) AF: 0.198 AC: 3025 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.160 AC: 554 AN: 3466

East Asian (EAS) AF: 0.404 AC: 2087 AN: 5170

South Asian (SAS) AF: 0.294 AC: 1416 AN: 4820

European-Finnish (FIN) AF: 0.182 AC: 1930 AN: 10584

Middle Eastern (MID) AF: 0.163 AC: 48 AN: 294

European-Non Finnish (NFE) AF: 0.203 AC: 13762 AN: 67956

Other (OTH) AF: 0.215 AC: 453 AN: 2110

Alfa AF: 0.219 Hom.: 17068

Bravo AF: 0.252

Asia WGS AF: 0.333 AC: 1157 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.0080
DANN	Benign	0.38
PhyloP100		-2.2

Splicing

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

Other links and lift over

dbSNP: rs868795; hg19: chr12-121371233;