chr12-115453598-C-T

Variant names:

• chr12-115453598-C-T
• rs7315438
• ENST00000793387.1:n.150-46267G>A

Variant summary

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

The ENST00000793387.1(ENSG00000303287):​n.150-46267G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.609 in 152,086 control chromosomes in the GnomAD database, including 29,126 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 0.61 (29126 hom., cov: 33)
• Consequence: ENSG00000303287 ENST00000793387.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.25
• Publications: 30 publications found

Genes affected

ENSG00000303287 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.745 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000793387.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000303287	ENST00000793387.1		n.150-46267G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.609 AC: 92522 AN: 151966 Hom.: 29093 Cov.: 33

Gnomad AFR AF: 0.752

Gnomad AMI AF: 0.591

Gnomad AMR AF: 0.460

Gnomad ASJ AF: 0.516

Gnomad EAS AF: 0.356

Gnomad SAS AF: 0.481

Gnomad FIN AF: 0.694

Gnomad MID AF: 0.589

Gnomad NFE AF: 0.577

Gnomad OTH AF: 0.553

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

GnomAD4 genome AF: 0.609 AC: 92616 AN: 152086 Hom.: 29126 Cov.: 33 AF XY: 0.608 AC XY: 45204 AN XY: 74352

African (AFR) AF: 0.752 AC: 31195 AN: 41484

American (AMR) AF: 0.461 AC: 7045 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.516 AC: 1788 AN: 3468

East Asian (EAS) AF: 0.356 AC: 1843 AN: 5172

South Asian (SAS) AF: 0.483 AC: 2324 AN: 4816

European-Finnish (FIN) AF: 0.694 AC: 7331 AN: 10568

Middle Eastern (MID) AF: 0.578 AC: 170 AN: 294

European-Non Finnish (NFE) AF: 0.577 AC: 39220 AN: 67974

Other (OTH) AF: 0.551 AC: 1165 AN: 2114

Alfa AF: 0.574 Hom.: 46589

Bravo AF: 0.596

Asia WGS AF: 0.445 AC: 1552 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.23
DANN	Benign	0.42
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs7315438; hg19: chr12-115891403;