rs12313095

Variant names:

• chr12-114009055-G-A
• rs12313095
• ENST00000789884.1:n.-162G>A

Your query was ambiguous. Multiple possible variants found:

• chr12-114009055-G-A
• chr12-114009055-G-C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000789884.1(ENSG00000302823):​n.-162G>A variant causes a upstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.354 in 152,052 control chromosomes in the GnomAD database, including 9,630 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 0.35 (9630 hom., cov: 32)
• Consequence: ENSG00000302823 ENST00000789884.1 upstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.452
• Publications: 1 publications found

Genes affected

ENSG00000302823 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.445 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000302823	ENST00000789884.1	n.-162G>A		upstream_gene_variant

Frequencies

GnomAD3 genomes AF: 0.354 AC: 53732 AN: 151934 Hom.: 9624 Cov.: 32

Gnomad AFR AF: 0.318

Gnomad AMI AF: 0.330

Gnomad AMR AF: 0.340

Gnomad ASJ AF: 0.337

Gnomad EAS AF: 0.461

Gnomad SAS AF: 0.297

Gnomad FIN AF: 0.347

Gnomad MID AF: 0.320

Gnomad NFE AF: 0.377

Gnomad OTH AF: 0.357

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

GnomAD4 genome AF: 0.354 AC: 53771 AN: 152052 Hom.: 9630 Cov.: 32 AF XY: 0.353 AC XY: 26210 AN XY: 74344

African (AFR) AF: 0.318 AC: 13189 AN: 41472

American (AMR) AF: 0.340 AC: 5197 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.337 AC: 1168 AN: 3466

East Asian (EAS) AF: 0.461 AC: 2387 AN: 5180

South Asian (SAS) AF: 0.296 AC: 1428 AN: 4824

European-Finnish (FIN) AF: 0.347 AC: 3658 AN: 10556

Middle Eastern (MID) AF: 0.316 AC: 93 AN: 294

European-Non Finnish (NFE) AF: 0.377 AC: 25593 AN: 67944

Other (OTH) AF: 0.358 AC: 757 AN: 2116

Alfa AF: 0.364 Hom.: 17479

Bravo AF: 0.354

Asia WGS AF: 0.372 AC: 1292 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	4.4
DANN	Benign	0.55
PhyloP100		0.45

Splicing

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

Other links and lift over

dbSNP: rs12313095; hg19: chr12-114446860;