rs1498759

Variant names:

• chr12-115386277-C-T
• rs1498759
• ENST00000793388.1:n.240-12390G>A

Variant summary

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

The ENST00000793388.1(ENSG00000303287):​n.240-12390G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.369 in 151,616 control chromosomes in the GnomAD database, including 10,643 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 0.37 (10643 hom., cov: 31)
• Consequence: ENSG00000303287 ENST00000793388.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.235
• Publications: 2 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=-0.99).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.579 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000793388.1. 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	ENST00000793388.1		n.240-12390G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.369 AC: 55912 AN: 151500 Hom.: 10637 Cov.: 31

Gnomad AFR AF: 0.294

Gnomad AMI AF: 0.333

Gnomad AMR AF: 0.366

Gnomad ASJ AF: 0.414

Gnomad EAS AF: 0.333

Gnomad SAS AF: 0.598

Gnomad FIN AF: 0.389

Gnomad MID AF: 0.421

Gnomad NFE AF: 0.396

Gnomad OTH AF: 0.389

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

GnomAD4 genome AF: 0.369 AC: 55937 AN: 151616 Hom.: 10643 Cov.: 31 AF XY: 0.371 AC XY: 27510 AN XY: 74062

African (AFR) AF: 0.294 AC: 12173 AN: 41344

American (AMR) AF: 0.366 AC: 5580 AN: 15242

Ashkenazi Jewish (ASJ) AF: 0.414 AC: 1437 AN: 3468

East Asian (EAS) AF: 0.332 AC: 1712 AN: 5152

South Asian (SAS) AF: 0.598 AC: 2875 AN: 4810

European-Finnish (FIN) AF: 0.389 AC: 4066 AN: 10464

Middle Eastern (MID) AF: 0.418 AC: 123 AN: 294

European-Non Finnish (NFE) AF: 0.396 AC: 26851 AN: 67824

Other (OTH) AF: 0.387 AC: 816 AN: 2106

Alfa AF: 0.384 Hom.: 5721

Bravo AF: 0.356

Asia WGS AF: 0.457 AC: 1585 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.3
DANN	Benign	0.69
PhyloP100		-0.23

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs1498759;

hg19: chr12-115824082;