rs12466517

Variant names:

• chr2-118072815-C-A
• rs12466517
• ENST00000747789.1:n.231+14698G>T

Your query was ambiguous. Multiple possible variants found:

• chr2-118072815-C-A
• chr2-118072815-C-T

Variant summary

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

The ENST00000747789.1(ENSG00000297418):​n.231+14698G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.412 in 151,986 control chromosomes in the GnomAD database, including 13,329 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 (13329 hom., cov: 32)
• Consequence: ENSG00000297418 ENST00000747789.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0900
• Publications: 3 publications found

Genes affected

ENSG00000297418 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.511 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107985940	XR_001739662.3	n.182-9799G>T		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000297418	ENST00000747789.1	n.231+14698G>T		intron_variant	Intron 2 of 4
ENSG00000297418	ENST00000747790.1	n.104+15436G>T		intron_variant	Intron 1 of 2
ENSG00000297418	ENST00000747791.1	n.331+1679G>T		intron_variant	Intron 3 of 4

Frequencies

GnomAD3 genomes AF: 0.412 AC: 62636 AN: 151866 Hom.: 13321 Cov.: 32

Gnomad AFR AF: 0.517

Gnomad AMI AF: 0.425

Gnomad AMR AF: 0.404

Gnomad ASJ AF: 0.412

Gnomad EAS AF: 0.431

Gnomad SAS AF: 0.413

Gnomad FIN AF: 0.276

Gnomad MID AF: 0.405

Gnomad NFE AF: 0.371

Gnomad OTH AF: 0.393

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

GnomAD4 genome AF: 0.412 AC: 62673 AN: 151986 Hom.: 13329 Cov.: 32 AF XY: 0.408 AC XY: 30321 AN XY: 74284

African (AFR) AF: 0.516 AC: 21400 AN: 41438

American (AMR) AF: 0.404 AC: 6167 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.412 AC: 1428 AN: 3466

East Asian (EAS) AF: 0.431 AC: 2220 AN: 5154

South Asian (SAS) AF: 0.412 AC: 1986 AN: 4816

European-Finnish (FIN) AF: 0.276 AC: 2910 AN: 10558

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

European-Non Finnish (NFE) AF: 0.371 AC: 25234 AN: 67970

Other (OTH) AF: 0.387 AC: 818 AN: 2112

Alfa AF: 0.299 Hom.: 949

Bravo AF: 0.427

Asia WGS AF: 0.395 AC: 1376 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	4.7
DANN	Benign	0.45
PhyloP100		0.090

Splicing

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

Other links and lift over

dbSNP: rs12466517; hg19: chr2-118830391;