12-34098085-C-T

Position:

• chr12-34098085-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 0.175 in 152,062 control chromosomes in the GnomAD database, including 2,413 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 0.18 (2413 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.128

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.189 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.34098085C>T		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.176 AC: 26672 AN: 151944 Hom.: 2414 Cov.: 32

Gnomad AFR AF: 0.169

Gnomad AMI AF: 0.322

Gnomad AMR AF: 0.158

Gnomad ASJ AF: 0.188

Gnomad EAS AF: 0.111

Gnomad SAS AF: 0.0948

Gnomad FIN AF: 0.178

Gnomad MID AF: 0.130

Gnomad NFE AF: 0.191

Gnomad OTH AF: 0.175

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

GnomAD4 genome AF: 0.175 AC: 26669 AN: 152062 Hom.: 2413 Cov.: 32 AF XY: 0.174 AC XY: 12933 AN XY: 74336

Gnomad4 AFR AF: 0.169

Gnomad4 AMR AF: 0.158

Gnomad4 ASJ AF: 0.188

Gnomad4 EAS AF: 0.110

Gnomad4 SAS AF: 0.0951

Gnomad4 FIN AF: 0.178

Gnomad4 NFE AF: 0.191

Gnomad4 OTH AF: 0.173

Alfa AF: 0.194 Hom.: 371

Bravo AF: 0.175

Asia WGS AF: 0.113 AC: 391 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	7.1
DANN	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1511547; hg19: chr12-34251020;