rs7956193

Positions:

• chr12-113053979-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 0.285 in 150,914 control chromosomes in the GnomAD database, including 6,539 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 0.29 (6538 hom., cov: 27)
  • Exomes 𝑓: 0.33 (1 hom.)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0650

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.315 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.113053979C>T		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.286 AC: 43055 AN: 150790 Hom.: 6541 Cov.: 27

Gnomad AFR AF: 0.281

Gnomad AMI AF: 0.439

Gnomad AMR AF: 0.279

Gnomad ASJ AF: 0.462

Gnomad EAS AF: 0.0234

Gnomad SAS AF: 0.137

Gnomad FIN AF: 0.217

Gnomad MID AF: 0.438

Gnomad NFE AF: 0.318

Gnomad OTH AF: 0.313

GnomAD4 exome AF: 0.333 AC: 2 AN: 6 Hom.: 1 AF XY: 1.00 AC XY: 2 AN XY: 2

Gnomad4 NFE exome AF: 0.333

GnomAD4 genome AF: 0.285 AC: 43070 AN: 150908 Hom.: 6538 Cov.: 27 AF XY: 0.274 AC XY: 20187 AN XY: 73578

Gnomad4 AFR AF: 0.280

Gnomad4 AMR AF: 0.278

Gnomad4 ASJ AF: 0.462

Gnomad4 EAS AF: 0.0235

Gnomad4 SAS AF: 0.138

Gnomad4 FIN AF: 0.217

Gnomad4 NFE AF: 0.318

Gnomad4 OTH AF: 0.314

Alfa AF: 0.301 Hom.: 856

Bravo AF: 0.293

Asia WGS AF: 0.128 AC: 446 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	4.3
DANN	Benign	0.33

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7956193; hg19: chr12-113491784;