chr12-114267781-C-T

Variant names:

• chr12-114267781-C-T
• rs1920592

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 0.192 in 152,188 control chromosomes in the GnomAD database, including 3,545 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 0.19 (3545 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.65
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.517 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: 0.192 AC: 29206 AN: 152070 Hom.: 3550 Cov.: 32

Gnomad AFR AF: 0.0637

Gnomad AMI AF: 0.0877

Gnomad AMR AF: 0.220

Gnomad ASJ AF: 0.157

Gnomad EAS AF: 0.534

Gnomad SAS AF: 0.313

Gnomad FIN AF: 0.244

Gnomad MID AF: 0.209

Gnomad NFE AF: 0.225

Gnomad OTH AF: 0.169

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

GnomAD4 genome AF: 0.192 AC: 29188 AN: 152188 Hom.: 3545 Cov.: 32 AF XY: 0.198 AC XY: 14707 AN XY: 74390

African (AFR) AF: 0.0636 AC: 2641 AN: 41554

American (AMR) AF: 0.219 AC: 3354 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.157 AC: 546 AN: 3470

East Asian (EAS) AF: 0.534 AC: 2748 AN: 5148

South Asian (SAS) AF: 0.312 AC: 1505 AN: 4822

European-Finnish (FIN) AF: 0.244 AC: 2582 AN: 10594

Middle Eastern (MID) AF: 0.207 AC: 61 AN: 294

European-Non Finnish (NFE) AF: 0.225 AC: 15314 AN: 67996

Other (OTH) AF: 0.169 AC: 357 AN: 2114

Alfa AF: 0.164 Hom.: 1041

Bravo AF: 0.184

Asia WGS AF: 0.341 AC: 1186 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	14
DANN	Benign	0.77
PhyloP100		1.6

Splicing

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

Other links and lift over

dbSNP: rs1920592; hg19: chr12-114705586;