12-127308069-C-T

Variant names:

• chr12-127308069-C-T
• rs1823172

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.169 in 152,130 control chromosomes in the GnomAD database, including 2,993 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 0.17 (2993 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.38

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.05).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.31 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: 0.169 AC: 25633 AN: 152010 Hom.: 2973 Cov.: 33

Gnomad AFR AF: 0.314

Gnomad AMI AF: 0.0548

Gnomad AMR AF: 0.146

Gnomad ASJ AF: 0.157

Gnomad EAS AF: 0.288

Gnomad SAS AF: 0.220

Gnomad FIN AF: 0.143

Gnomad MID AF: 0.199

Gnomad NFE AF: 0.0789

Gnomad OTH AF: 0.151

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

GnomAD4 genome AF: 0.169 AC: 25700 AN: 152130 Hom.: 2993 Cov.: 33 AF XY: 0.174 AC XY: 12924 AN XY: 74370

Gnomad4 AFR AF: 0.314

Gnomad4 AMR AF: 0.147

Gnomad4 ASJ AF: 0.157

Gnomad4 EAS AF: 0.289

Gnomad4 SAS AF: 0.218

Gnomad4 FIN AF: 0.143

Gnomad4 NFE AF: 0.0790

Gnomad4 OTH AF: 0.155

Alfa AF: 0.103 Hom.: 1526

Bravo AF: 0.176

Asia WGS AF: 0.277 AC: 967 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.31
DANN	Benign	0.37

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1823172; hg19: chr12-127792614;