rs12513663

Variant names:

• chr5-124496959-C-T
• rs12513663
• ENST00000503145.1:n.387-3774G>A

Variant summary

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

The ENST00000503145.1(ENSG00000248296):​n.387-3774G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.259 in 151,956 control chromosomes in the GnomAD database, including 6,490 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 0.26 (6490 hom., cov: 31)
• Consequence: ENSG00000248296 ENST00000503145.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.436
• Publications: 5 publications found

Genes affected

ENSG00000248296 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.601 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000503145.1. 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
	ENSG00000248296	ENST00000503145.1	TSL:3	n.387-3774G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.259 AC: 39283 AN: 151838 Hom.: 6470 Cov.: 31

Gnomad AFR AF: 0.0836

Gnomad AMI AF: 0.275

Gnomad AMR AF: 0.380

Gnomad ASJ AF: 0.242

Gnomad EAS AF: 0.618

Gnomad SAS AF: 0.464

Gnomad FIN AF: 0.382

Gnomad MID AF: 0.166

Gnomad NFE AF: 0.278

Gnomad OTH AF: 0.255

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

GnomAD4 genome AF: 0.259 AC: 39337 AN: 151956 Hom.: 6490 Cov.: 31 AF XY: 0.274 AC XY: 20342 AN XY: 74242

African (AFR) AF: 0.0839 AC: 3476 AN: 41448

American (AMR) AF: 0.381 AC: 5825 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.242 AC: 838 AN: 3468

East Asian (EAS) AF: 0.619 AC: 3184 AN: 5146

South Asian (SAS) AF: 0.463 AC: 2234 AN: 4820

European-Finnish (FIN) AF: 0.382 AC: 4025 AN: 10534

Middle Eastern (MID) AF: 0.168 AC: 49 AN: 292

European-Non Finnish (NFE) AF: 0.278 AC: 18901 AN: 67958

Other (OTH) AF: 0.263 AC: 555 AN: 2108

Alfa AF: 0.213 Hom.: 1810

Bravo AF: 0.246

Asia WGS AF: 0.532 AC: 1849 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.0
DANN	Benign	0.67
PhyloP100		-0.44

Splicing

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

Other links and lift over

dbSNP: rs12513663; hg19: chr5-123832652;