13-33134652-C-T

Variant summary

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

The NM_178006.4(STARD13):​c.388-4363G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0811 in 152,098 control chromosomes in the GnomAD database, including 626 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 0.081 ( 626 hom., cov: 33)

Consequence

STARD13
NM_178006.4 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.30
Variant links:
Genes affected
STARD13 (HGNC:19164): (StAR related lipid transfer domain containing 13) This gene encodes a protein which contains an N-terminal sterile alpha motif (SAM) for protein-protein interactions, followed by an ATP/GTP-binding motif, a GTPase-activating protein (GAP) domain, and a C-terminal STAR-related lipid transfer (START) domain. It may be involved in regulation of cytoskeletal reorganization, cell proliferation, and cell motility, and acts as a tumor suppressor in hepatoma cells. The gene is located in a region of chromosome 13 that is associated with loss of heterozygosity in hepatocellular carcinomas. Alternatively spliced transcript variants encoding different isoforms have been described for this gene. [provided by RefSeq, Aug 2011]

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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 (EAS) allele frequency at 95% confidence interval = 0.235 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
STARD13NM_178006.4 linkc.388-4363G>A intron_variant Intron 4 of 13 ENST00000336934.10 NP_821074.1 Q9Y3M8-1A0A024RDV4

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
STARD13ENST00000336934.10 linkc.388-4363G>A intron_variant Intron 4 of 13 1 NM_178006.4 ENSP00000338785.4 Q9Y3M8-1
STARD13ENST00000255486.8 linkc.364-4363G>A intron_variant Intron 4 of 13 1 ENSP00000255486.4 Q9Y3M8-2
STARD13ENST00000567873.2 linkc.343-4363G>A intron_variant Intron 4 of 13 1 ENSP00000456233.2 H3BRG5
STARD13ENST00000399365.7 linkc.34-4363G>A intron_variant Intron 4 of 13 1 ENSP00000382300.3 Q9Y3M8-3

Frequencies

GnomAD3 genomes
AF:
0.0811
AC:
12324
AN:
151980
Hom.:
626
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.0697
Gnomad AMI
AF:
0.0702
Gnomad AMR
AF:
0.119
Gnomad ASJ
AF:
0.0752
Gnomad EAS
AF:
0.246
Gnomad SAS
AF:
0.0950
Gnomad FIN
AF:
0.0949
Gnomad MID
AF:
0.0348
Gnomad NFE
AF:
0.0641
Gnomad OTH
AF:
0.0952
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.0811
AC:
12340
AN:
152098
Hom.:
626
Cov.:
33
AF XY:
0.0835
AC XY:
6210
AN XY:
74352
show subpopulations
Gnomad4 AFR
AF:
0.0697
Gnomad4 AMR
AF:
0.119
Gnomad4 ASJ
AF:
0.0752
Gnomad4 EAS
AF:
0.246
Gnomad4 SAS
AF:
0.0951
Gnomad4 FIN
AF:
0.0949
Gnomad4 NFE
AF:
0.0641
Gnomad4 OTH
AF:
0.0952
Alfa
AF:
0.0727
Hom.:
235
Bravo
AF:
0.0859
Asia WGS
AF:
0.156
AC:
544
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
0.63
DANN
Benign
0.51

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: rs10492402; hg19: chr13-33708789; API