12-119965993-C-T

Position:

• chr12-119965993-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 0.132 in 151,790 control chromosomes in the GnomAD database, including 1,646 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 (1646 hom., cov: 31)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.37

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.344 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.119965993C>T		intergenic_region
LOC112268087	XR_002957390.2	n.312-9025C>T		intron_variant
LOC112268087	XR_002957391.2	n.398-9025C>T		intron_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.132 AC: 19987 AN: 151674 Hom.: 1634 Cov.: 31

Gnomad AFR AF: 0.0801

Gnomad AMI AF: 0.0888

Gnomad AMR AF: 0.206

Gnomad ASJ AF: 0.0591

Gnomad EAS AF: 0.357

Gnomad SAS AF: 0.166

Gnomad FIN AF: 0.135

Gnomad MID AF: 0.0573

Gnomad NFE AF: 0.132

Gnomad OTH AF: 0.116

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

GnomAD4 genome AF: 0.132 AC: 20023 AN: 151790 Hom.: 1646 Cov.: 31 AF XY: 0.136 AC XY: 10107 AN XY: 74152

Gnomad4 AFR AF: 0.0801

Gnomad4 AMR AF: 0.206

Gnomad4 ASJ AF: 0.0591

Gnomad4 EAS AF: 0.358

Gnomad4 SAS AF: 0.166

Gnomad4 FIN AF: 0.135

Gnomad4 NFE AF: 0.132

Gnomad4 OTH AF: 0.122

Alfa AF: 0.130 Hom.: 656

Bravo AF: 0.135

Asia WGS AF: 0.261 AC: 905 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.6
DANN	Benign	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10774538; hg19: chr12-120403797;