GeneBe

ENST00000451987.5:c.-172-10158G>A

Variant names:

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000451987.5(SPC25):​c.-172-10158G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.253 in 151,894 control chromosomes in the GnomAD database, including 5,074 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 0.25 ( 5074 hom., cov: 32)

Consequence

SPC25
ENST00000451987.5 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.140

Publications

43 publications found
Variant links:
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]

Genome browser will be placed here

ACMG classification

Classification was made for transcript

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

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.84).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.382 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
SPC25ENST00000451987.5 linkc.-172-10158G>A intron_variant Intron 1 of 4 3 ENSP00000393322.1 C9JW94
SPC25ENST00000472216.2 linkn.177-10158G>A intron_variant Intron 1 of 5 5

Frequencies

GnomAD3 genomes
AF:
0.253
AC:
38325
AN:
151772
Hom.:
5070
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.306
Gnomad AMI
AF:
0.421
Gnomad AMR
AF:
0.213
Gnomad ASJ
AF:
0.246
Gnomad EAS
AF:
0.396
Gnomad SAS
AF:
0.224
Gnomad FIN
AF:
0.177
Gnomad MID
AF:
0.222
Gnomad NFE
AF:
0.230
Gnomad OTH
AF:
0.255
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.253
AC:
38364
AN:
151894
Hom.:
5074
Cov.:
32
AF XY:
0.251
AC XY:
18635
AN XY:
74224
show subpopulations
African (AFR)
AF:
0.306
AC:
12676
AN:
41400
American (AMR)
AF:
0.212
AC:
3240
AN:
15258
Ashkenazi Jewish (ASJ)
AF:
0.246
AC:
851
AN:
3466
East Asian (EAS)
AF:
0.396
AC:
2046
AN:
5164
South Asian (SAS)
AF:
0.225
AC:
1080
AN:
4808
European-Finnish (FIN)
AF:
0.177
AC:
1860
AN:
10528
Middle Eastern (MID)
AF:
0.214
AC:
63
AN:
294
European-Non Finnish (NFE)
AF:
0.230
AC:
15622
AN:
67952
Other (OTH)
AF:
0.257
AC:
542
AN:
2112
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.502
Heterozygous variant carriers
0
1469
2937
4406
5874
7343
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
392
784
1176
1568
1960
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
Alfa
AF:
0.238
Hom.:
15742
Bravo
AF:
0.257
Asia WGS
AF:
0.282
AC:
978
AN:
3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.84
CADD
Benign
3.8
DANN
Benign
0.43
PhyloP100
-0.14
PromoterAI
0.0041
Neutral

Splicing

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

Publications

Other links and lift over

dbSNP: rs1402837; hg19: chr2-169757354; API