rs12513663

Variant names:

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

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

ENSG00000248296 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000248296	ENST00000503145.1	n.387-3774G>A		intron_variant	Intron 2 of 2	3

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

Gnomad4 AFR AF: 0.0839

Gnomad4 AMR AF: 0.381

Gnomad4 ASJ AF: 0.242

Gnomad4 EAS AF: 0.619

Gnomad4 SAS AF: 0.463

Gnomad4 FIN AF: 0.382

Gnomad4 NFE AF: 0.278

Gnomad4 OTH AF: 0.263

Alfa AF: 0.257 Hom.: 866

Bravo AF: 0.246

Asia WGS AF: 0.532 AC: 1849 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12513663; hg19: chr5-123832652;