rs868795

Positions:

• chr12-120933430-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 0.245 in 152,010 control chromosomes in the GnomAD database, including 4,992 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 0.24 (4992 hom., cov: 31)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.22

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.389 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.120933430C>T		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.245 AC: 37180 AN: 151892 Hom.: 4984 Cov.: 31

Gnomad AFR AF: 0.331

Gnomad AMI AF: 0.237

Gnomad AMR AF: 0.198

Gnomad ASJ AF: 0.160

Gnomad EAS AF: 0.404

Gnomad SAS AF: 0.294

Gnomad FIN AF: 0.182

Gnomad MID AF: 0.161

Gnomad NFE AF: 0.202

Gnomad OTH AF: 0.216

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

GnomAD4 genome AF: 0.245 AC: 37221 AN: 152010 Hom.: 4992 Cov.: 31 AF XY: 0.246 AC XY: 18267 AN XY: 74300

Gnomad4 AFR AF: 0.331

Gnomad4 AMR AF: 0.198

Gnomad4 ASJ AF: 0.160

Gnomad4 EAS AF: 0.404

Gnomad4 SAS AF: 0.294

Gnomad4 FIN AF: 0.182

Gnomad4 NFE AF: 0.203

Gnomad4 OTH AF: 0.215

Alfa AF: 0.211 Hom.: 7372

Bravo AF: 0.252

Asia WGS AF: 0.333 AC: 1157 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.0080
DANN	Benign	0.38

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs868795; hg19: chr12-121371233;