rs1463833

Variant names:

• chr12-115378637-A-G
• rs1463833
• ENST00000793388.1:n.240-4750T>C

Your query was ambiguous. Multiple possible variants found:

• chr12-115378637-A-G
• chr12-115378637-A-T

Variant summary

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

The ENST00000793388.1(ENSG00000303287):​n.240-4750T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.414 in 151,982 control chromosomes in the GnomAD database, including 13,213 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 0.41 (13213 hom., cov: 33)
• Consequence: ENSG00000303287 ENST00000793388.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0270
• 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=-0.86).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.559 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105370003	XR_945389.3	n.503-4750T>C		intron_variant	Intron 3 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000303287	ENST00000793388.1	n.240-4750T>C		intron_variant	Intron 1 of 1
ENSG00000303287	ENST00000793389.1	n.205+3949T>C		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.414 AC: 62818 AN: 151866 Hom.: 13203 Cov.: 33

Gnomad AFR AF: 0.391

Gnomad AMI AF: 0.402

Gnomad AMR AF: 0.469

Gnomad ASJ AF: 0.407

Gnomad EAS AF: 0.340

Gnomad SAS AF: 0.576

Gnomad FIN AF: 0.425

Gnomad MID AF: 0.427

Gnomad NFE AF: 0.407

Gnomad OTH AF: 0.427

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

GnomAD4 genome AF: 0.414 AC: 62865 AN: 151982 Hom.: 13213 Cov.: 33 AF XY: 0.416 AC XY: 30875 AN XY: 74274

African (AFR) AF: 0.391 AC: 16194 AN: 41424

American (AMR) AF: 0.470 AC: 7173 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.407 AC: 1413 AN: 3468

East Asian (EAS) AF: 0.339 AC: 1747 AN: 5154

South Asian (SAS) AF: 0.576 AC: 2776 AN: 4816

European-Finnish (FIN) AF: 0.425 AC: 4488 AN: 10568

Middle Eastern (MID) AF: 0.425 AC: 125 AN: 294

European-Non Finnish (NFE) AF: 0.407 AC: 27691 AN: 67976

Other (OTH) AF: 0.424 AC: 892 AN: 2102

Alfa AF: 0.407 Hom.: 49878

Bravo AF: 0.410

Asia WGS AF: 0.462 AC: 1607 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.58
DANN	Benign	0.53
PhyloP100		0.027

Splicing

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

Other links and lift over

dbSNP: rs1463833; hg19: chr12-115816442; COSMIC: COSV107990994;