rs13431652

Variant names:

• chr2-168896905-T-C
• rs13431652
• ENST00000861849.1:c.-172-6219A>G

Variant summary

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

The ENST00000451987.5(SPC25):​c.-172-6219A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.243 in 152,068 control chromosomes in the GnomAD database, including 4,880 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 0.24 (4880 hom., cov: 31)
• Consequence: SPC25 ENST00000451987.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.299
• Publications: 20 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=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.304 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000451987.5. 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
	SPC25	ENST00000861849.1		c.-172-6219A>G		intron	N/A	ENSP00000531908.1
	SPC25	ENST00000861850.1		c.-14-7372A>G		intron	N/A	ENSP00000531909.1
	SPC25	ENST00000451987.5	TSL:3	c.-172-6219A>G		intron	N/A	ENSP00000393322.1	C9JW94

Frequencies

GnomAD3 genomes AF: 0.243 AC: 36884 AN: 151950 Hom.: 4880 Cov.: 31

Gnomad AFR AF: 0.170

Gnomad AMI AF: 0.222

Gnomad AMR AF: 0.209

Gnomad ASJ AF: 0.217

Gnomad EAS AF: 0.0564

Gnomad SAS AF: 0.169

Gnomad FIN AF: 0.295

Gnomad MID AF: 0.266

Gnomad NFE AF: 0.308

Gnomad OTH AF: 0.243

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

GnomAD4 genome AF: 0.243 AC: 36901 AN: 152068 Hom.: 4880 Cov.: 31 AF XY: 0.238 AC XY: 17682 AN XY: 74334

African (AFR) AF: 0.170 AC: 7038 AN: 41510

American (AMR) AF: 0.209 AC: 3192 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.217 AC: 751 AN: 3466

East Asian (EAS) AF: 0.0566 AC: 293 AN: 5180

South Asian (SAS) AF: 0.169 AC: 816 AN: 4820

European-Finnish (FIN) AF: 0.295 AC: 3112 AN: 10556

Middle Eastern (MID) AF: 0.252 AC: 74 AN: 294

European-Non Finnish (NFE) AF: 0.308 AC: 20906 AN: 67950

Other (OTH) AF: 0.245 AC: 517 AN: 2110

Alfa AF: 0.265 Hom.: 934

Bravo AF: 0.232

Asia WGS AF: 0.137 AC: 478 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.2
DANN	Benign	0.64
PhyloP100		-0.30

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs13431652;

hg19: chr2-169753415;