chr12-126826075-C-T

Variant names:

• chr12-126826075-C-T
• rs12827056

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 0.254 in 151,932 control chromosomes in the GnomAD database, including 5,954 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 0.25 (5954 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.26

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.341 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: 0.254 AC: 38569 AN: 151814 Hom.: 5953 Cov.: 32

Gnomad AFR AF: 0.114

Gnomad AMI AF: 0.0976

Gnomad AMR AF: 0.227

Gnomad ASJ AF: 0.325

Gnomad EAS AF: 0.00193

Gnomad SAS AF: 0.329

Gnomad FIN AF: 0.330

Gnomad MID AF: 0.236

Gnomad NFE AF: 0.345

Gnomad OTH AF: 0.289

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

GnomAD4 genome AF: 0.254 AC: 38565 AN: 151932 Hom.: 5954 Cov.: 32 AF XY: 0.253 AC XY: 18751 AN XY: 74252

Gnomad4 AFR AF: 0.114

Gnomad4 AMR AF: 0.227

Gnomad4 ASJ AF: 0.325

Gnomad4 EAS AF: 0.00193

Gnomad4 SAS AF: 0.330

Gnomad4 FIN AF: 0.330

Gnomad4 NFE AF: 0.345

Gnomad4 OTH AF: 0.284

Alfa AF: 0.325 Hom.: 4389

Bravo AF: 0.236

Asia WGS AF: 0.133 AC: 460 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	6.3
DANN	Benign	0.82

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12827056; hg19: chr12-127310621;