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GeneBe

13-36302242-A-G

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1

The NM_015087.5(SPART):c.*2123T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.242 in 151,786 control chromosomes in the GnomAD database, including 4,769 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.24 ( 4769 hom., cov: 32)
Failed GnomAD Quality Control

Consequence

SPART
NM_015087.5 3_prime_UTR

Scores

2

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.0340
Variant links:
Genes affected
SPART (HGNC:18514): (spartin) This gene encodes a protein containing a MIT (Microtubule Interacting and Trafficking molecule) domain, and is implicated in regulating endosomal trafficking and mitochondria function. The protein localizes to mitochondria and partially co-localizes with microtubules. Stimulation with epidermal growth factor (EGF) results in protein translocation to the plasma membrane, and the protein functions in the degradation and intracellular trafficking of EGF receptor. Multiple alternatively spliced variants, encoding the same protein, have been identified. Mutations associated with this gene cause autosomal recessive spastic paraplegia 20 (Troyer syndrome). [provided by RefSeq, Nov 2008]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.91).
BP6
Variant 13-36302242-A-G is Benign according to our data. Variant chr13-36302242-A-G is described in ClinVar as [Benign]. Clinvar id is 311743.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.487 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
SPARTNM_015087.5 linkuse as main transcriptc.*2123T>C 3_prime_UTR_variant 9/9 ENST00000438666.7

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
SPARTENST00000438666.7 linkuse as main transcriptc.*2123T>C 3_prime_UTR_variant 9/91 NM_015087.5 P1
SPARTENST00000451493.5 linkuse as main transcriptc.*2123T>C 3_prime_UTR_variant 9/91 P1
SPARTENST00000355182.8 linkuse as main transcriptc.*2123T>C 3_prime_UTR_variant 9/95 P1
SPARTENST00000650221.1 linkuse as main transcriptc.*2123T>C 3_prime_UTR_variant 10/10 P1

Frequencies

GnomAD3 genomes
AF:
0.242
AC:
36694
AN:
151670
Hom.:
4775
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.152
Gnomad AMI
AF:
0.281
Gnomad AMR
AF:
0.290
Gnomad ASJ
AF:
0.220
Gnomad EAS
AF:
0.505
Gnomad SAS
AF:
0.280
Gnomad FIN
AF:
0.228
Gnomad MID
AF:
0.216
Gnomad NFE
AF:
0.267
Gnomad OTH
AF:
0.218
GnomAD4 exome
Data not reliable, filtered out with message: AC0
AC:
0
AN:
0
Hom.:
0
Cov.:
0
AC XY:
0
AN XY:
0
GnomAD4 genome
AF:
0.242
AC:
36709
AN:
151786
Hom.:
4769
Cov.:
32
AF XY:
0.244
AC XY:
18132
AN XY:
74186
show subpopulations
Gnomad4 AFR
AF:
0.152
Gnomad4 AMR
AF:
0.291
Gnomad4 ASJ
AF:
0.220
Gnomad4 EAS
AF:
0.503
Gnomad4 SAS
AF:
0.280
Gnomad4 FIN
AF:
0.228
Gnomad4 NFE
AF:
0.267
Gnomad4 OTH
AF:
0.221
Alfa
AF:
0.184
Hom.:
650
Bravo
AF:
0.242
Asia WGS
AF:
0.399
AC:
1389
AN:
3476

ClinVar

Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

Troyer syndrome Benign:1
Benign, criteria provided, single submitterclinical testingIllumina Laboratory Services, IlluminaJan 13, 2018This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.91
Cadd
Benign
1.3
Dann
Benign
0.61

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

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: rs78129833; hg19: chr13-36876379; COSMIC: COSV53485210; COSMIC: COSV53485210; API