12-108029499-C-T

Position:

• chr12-108029499-C-T

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 0.129 in 151,964 control chromosomes in the GnomAD database, including 3,175 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 0.13 (3175 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0990

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.6).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.354 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.129 AC: 19560 AN: 151844 Hom.: 3159 Cov.: 32

Gnomad AFR AF: 0.359

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.143

Gnomad ASJ AF: 0.00374

Gnomad EAS AF: 0.283

Gnomad SAS AF: 0.130

Gnomad FIN AF: 0.00850

Gnomad MID AF: 0.0222

Gnomad NFE AF: 0.00222

Gnomad OTH AF: 0.103

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

GnomAD4 genome AF: 0.129 AC: 19621 AN: 151964 Hom.: 3175 Cov.: 32 AF XY: 0.130 AC XY: 9628 AN XY: 74268

Gnomad4 AFR AF: 0.359

Gnomad4 AMR AF: 0.143

Gnomad4 ASJ AF: 0.00374

Gnomad4 EAS AF: 0.284

Gnomad4 SAS AF: 0.129

Gnomad4 FIN AF: 0.00850

Gnomad4 NFE AF: 0.00222

Gnomad4 OTH AF: 0.104

Alfa AF: 0.0251 Hom.: 857

Bravo AF: 0.151

Asia WGS AF: 0.193 AC: 672 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.60
CADD	Benign	11
DANN	Benign	0.77

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7971309; hg19: chr12-108423276;