rs13387347

Variant names:

• chr2-168898336-T-C
• rs13387347
• ENST00000451987.5:c.-172-7650A>G

Variant summary

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

The ENST00000451987.5(SPC25):​c.-172-7650A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.486 in 151,834 control chromosomes in the GnomAD database, including 18,302 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 0.49 (18302 hom., cov: 30)
• Consequence: SPC25 ENST00000451987.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.531
• Publications: 21 publications found

Genes affected

SPC25 (HGNC:24031): (SPC25 component of NDC80 kinetochore complex) This gene encodes a protein that may be involved in kinetochore-microtubule interaction and spindle checkpoint activity. [provided by RefSeq, Jul 2008]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.542 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
SPC25	ENST00000451987.5	c.-172-7650A>G		intron_variant	Intron 1 of 4	3		ENSP00000393322.1
SPC25	ENST00000472216.2	n.177-7650A>G		intron_variant	Intron 1 of 5	5

Frequencies

GnomAD3 genomes AF: 0.486 AC: 73752 AN: 151714 Hom.: 18292 Cov.: 30

Gnomad AFR AF: 0.424

Gnomad AMI AF: 0.665

Gnomad AMR AF: 0.418

Gnomad ASJ AF: 0.465

Gnomad EAS AF: 0.455

Gnomad SAS AF: 0.397

Gnomad FIN AF: 0.481

Gnomad MID AF: 0.478

Gnomad NFE AF: 0.547

Gnomad OTH AF: 0.494

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

GnomAD4 genome AF: 0.486 AC: 73796 AN: 151834 Hom.: 18302 Cov.: 30 AF XY: 0.479 AC XY: 35572 AN XY: 74222

African (AFR) AF: 0.424 AC: 17556 AN: 41388

American (AMR) AF: 0.417 AC: 6361 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.465 AC: 1611 AN: 3464

East Asian (EAS) AF: 0.456 AC: 2343 AN: 5142

South Asian (SAS) AF: 0.398 AC: 1915 AN: 4810

European-Finnish (FIN) AF: 0.481 AC: 5060 AN: 10530

Middle Eastern (MID) AF: 0.456 AC: 134 AN: 294

European-Non Finnish (NFE) AF: 0.547 AC: 37159 AN: 67914

Other (OTH) AF: 0.498 AC: 1052 AN: 2112

Alfa AF: 0.522 Hom.: 31368

Bravo AF: 0.476

Asia WGS AF: 0.415 AC: 1442 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.87
DANN	Benign	0.65
PhyloP100		-0.53

Splicing

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

Other links and lift over

dbSNP: rs13387347; hg19: chr2-169754846;