chr12-121132209-C-T

Position:

• chr12-121132209-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 0.386 in 152,006 control chromosomes in the GnomAD database, including 14,540 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 0.39 (14540 hom., cov: 31)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.393

Genes affected

(HGNC:):

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 (AFR) allele frequency at 95% confidence interval = 0.698 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.121132209C>T		intergenic_region
LOC105370032	XR_001749352.3	n.328-5368G>A		intron_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.386 AC: 58587 AN: 151888 Hom.: 14485 Cov.: 31

Gnomad AFR AF: 0.704

Gnomad AMI AF: 0.190

Gnomad AMR AF: 0.224

Gnomad ASJ AF: 0.201

Gnomad EAS AF: 0.382

Gnomad SAS AF: 0.376

Gnomad FIN AF: 0.346

Gnomad MID AF: 0.180

Gnomad NFE AF: 0.251

Gnomad OTH AF: 0.323

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

GnomAD4 genome AF: 0.386 AC: 58714 AN: 152006 Hom.: 14540 Cov.: 31 AF XY: 0.384 AC XY: 28545 AN XY: 74280

Gnomad4 AFR AF: 0.704

Gnomad4 AMR AF: 0.224

Gnomad4 ASJ AF: 0.201

Gnomad4 EAS AF: 0.382

Gnomad4 SAS AF: 0.378

Gnomad4 FIN AF: 0.346

Gnomad4 NFE AF: 0.251

Gnomad4 OTH AF: 0.325

Alfa AF: 0.243 Hom.: 1105

Bravo AF: 0.386

Asia WGS AF: 0.405 AC: 1407 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	0.99
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: rs2393799; hg19: chr12-121570012;