chr13-36302234-TTATC-T

Position:

• chr13-36302234-TTATC-T

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_Moderate BA1

The NM_015087.5(SPART):​c.*2127_*2130delGATA 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 151,704 control chromosomes in the GnomAD database, including 4,761 homozygotes. Variant has been reported in ClinVar as Likely benign (★).

• Frequency:
  • Genomes: 𝑓 0.24 (4761 hom., cov: 24)
  • Failed GnomAD Quality Control
• Consequence: SPART NM_015087.5 3_prime_UTR
• Clinical Significance: Likely benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.00700

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]

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP6: Variant 13-36302234-TTATC-T is Benign according to our data. Variant chr13-36302234-TTATC-T is described in ClinVar as [Likely_benign]. Clinvar id is 311742.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	Protein	UniProt
SPART	NM_015087.5	c.*2127_*2130delGATA		3_prime_UTR_variant	9/9	ENST00000438666.7	NP_055902.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SPART	ENST00000438666	c.*2127_*2130delGATA		3_prime_UTR_variant	9/9	1	NM_015087.5	ENSP00000406061.2
SPART	ENST00000451493	c.*2127_*2130delGATA		3_prime_UTR_variant	9/9	1		ENSP00000414147.1
SPART	ENST00000355182	c.*2127_*2130delGATA		3_prime_UTR_variant	9/9	5		ENSP00000347314.4
SPART	ENST00000650221	c.*2127_*2130delGATA		3_prime_UTR_variant	10/10			ENSP00000497209.1

Frequencies

GnomAD3 genomes AF: 0.242 AC: 36663 AN: 151586 Hom.: 4766 Cov.: 24

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

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

GnomAD4 genome AF: 0.242 AC: 36680 AN: 151704 Hom.: 4761 Cov.: 24 AF XY: 0.244 AC XY: 18115 AN XY: 74118

Gnomad4 AFR AF: 0.152

Gnomad4 AMR AF: 0.290

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: 0.242 Hom.: 575

Bravo AF: 0.241

Asia WGS AF: 0.399 AC: 1389 AN: 3476

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

Troyer syndrome Benign:1

Likely benign, criteria provided, single submitter

clinical testing

Illumina Laboratory Services, Illumina

Jun 14, 2016

- -

Computational scores

Source: dbNSFP v4.3

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

Other links and lift over

dbSNP: rs150662490; hg19: chr13-36876371;