rs13431652

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

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

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.299
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 made for transcript

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
SPC25ENST00000451987.5 linkuse as main transcriptc.-172-6219A>G intron_variant 3
SPC25ENST00000472216.2 linkuse as main transcriptn.177-6219A>G intron_variant, non_coding_transcript_variant 5

Frequencies

GnomAD3 genomes
AF:
0.243
AC:
36884
AN:
151950
Hom.:
4880
Cov.:
31
show subpopulations
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
show subpopulations
Gnomad4 AFR
AF:
0.170
Gnomad4 AMR
AF:
0.209
Gnomad4 ASJ
AF:
0.217
Gnomad4 EAS
AF:
0.0566
Gnomad4 SAS
AF:
0.169
Gnomad4 FIN
AF:
0.295
Gnomad4 NFE
AF:
0.308
Gnomad4 OTH
AF:
0.245
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 v4.3

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

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs13431652; hg19: chr2-169753415; API