rs7989684

Variant names:

• chr13-36358390-G-A
• rs7989684
• NM_001142294.2:c.-3+11699C>T

Variant summary

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

The NM_001142294.2(SPART):​c.-3+11699C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.987 in 152,320 control chromosomes in the GnomAD database, including 74,211 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 0.99 (74211 hom., cov: 33)
• Consequence: SPART NM_001142294.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.04
• Publications: 1 publications found

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]

SPART-AS1 (HGNC:39933): (SPART antisense RNA 1)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.993 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SPART	NM_001142294.2	c.-3+11699C>T		intron_variant	Intron 1 of 8		NP_001135766.1
SPART-AS1	NR_045180.1	n.78-2264G>A		intron_variant	Intron 1 of 5
SPART-AS1	NR_045181.1	n.78-7110G>A		intron_variant	Intron 1 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SPART	ENST00000355182.8	c.-3+11699C>T		intron_variant	Intron 1 of 8	5		ENSP00000347314.4
SPART	ENST00000650221.1	c.-3+10484C>T		intron_variant	Intron 2 of 9			ENSP00000497209.1
SPART-AS1	ENST00000379848.5	n.77-7110G>A		intron_variant	Intron 1 of 3	3

Frequencies

GnomAD3 genomes AF: 0.987 AC: 150227 AN: 152202 Hom.: 74158 Cov.: 33

Gnomad AFR AF: 0.955

Gnomad AMI AF: 1.00

Gnomad AMR AF: 0.995

Gnomad ASJ AF: 1.00

Gnomad EAS AF: 1.00

Gnomad SAS AF: 1.00

Gnomad FIN AF: 1.00

Gnomad MID AF: 0.991

Gnomad NFE AF: 1.00

Gnomad OTH AF: 0.992

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

GnomAD4 genome AF: 0.987 AC: 150339 AN: 152320 Hom.: 74211 Cov.: 33 AF XY: 0.987 AC XY: 73533 AN XY: 74474

African (AFR) AF: 0.955 AC: 39681 AN: 41552

American (AMR) AF: 0.995 AC: 15220 AN: 15296

Ashkenazi Jewish (ASJ) AF: 1.00 AC: 3470 AN: 3470

East Asian (EAS) AF: 1.00 AC: 5184 AN: 5184

South Asian (SAS) AF: 1.00 AC: 4830 AN: 4830

European-Finnish (FIN) AF: 1.00 AC: 10620 AN: 10620

Middle Eastern (MID) AF: 0.990 AC: 291 AN: 294

European-Non Finnish (NFE) AF: 1.00 AC: 68033 AN: 68048

Other (OTH) AF: 0.992 AC: 2098 AN: 2114

Alfa AF: 0.990 Hom.: 10960

Bravo AF: 0.985

Asia WGS AF: 0.997 AC: 3465 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.1
DANN	Benign	0.56
PhyloP100		-2.0
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs7989684; hg19: chr13-36932527;