rs4943110

Variant summary

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

The NM_001243476.3(STARD13):​c.31-21999A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.301 in 152,030 control chromosomes in the GnomAD database, including 7,632 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 0.30 ( 7632 hom., cov: 32)

Consequence

STARD13
NM_001243476.3 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.384
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=-0.96).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.385 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
STARD13NM_001243476.3 linkuse as main transcriptc.31-21999A>T intron_variant NP_001230405.1 Q9Y3M8
STARD13XM_047430759.1 linkuse as main transcriptc.166-21999A>T intron_variant XP_047286715.1
STARD13XM_017020835.3 linkuse as main transcriptc.31-21999A>T intron_variant XP_016876324.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
ENSG00000230490ENST00000454681.2 linkuse as main transcriptn.227-21999A>T intron_variant 5
ENSG00000230490ENST00000686875.1 linkuse as main transcriptn.279-21999A>T intron_variant

Frequencies

GnomAD3 genomes
AF:
0.301
AC:
45755
AN:
151912
Hom.:
7634
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.153
Gnomad AMI
AF:
0.364
Gnomad AMR
AF:
0.326
Gnomad ASJ
AF:
0.316
Gnomad EAS
AF:
0.223
Gnomad SAS
AF:
0.296
Gnomad FIN
AF:
0.310
Gnomad MID
AF:
0.342
Gnomad NFE
AF:
0.389
Gnomad OTH
AF:
0.319
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.301
AC:
45767
AN:
152030
Hom.:
7632
Cov.:
32
AF XY:
0.296
AC XY:
21967
AN XY:
74304
show subpopulations
Gnomad4 AFR
AF:
0.153
Gnomad4 AMR
AF:
0.326
Gnomad4 ASJ
AF:
0.316
Gnomad4 EAS
AF:
0.223
Gnomad4 SAS
AF:
0.297
Gnomad4 FIN
AF:
0.310
Gnomad4 NFE
AF:
0.389
Gnomad4 OTH
AF:
0.316
Alfa
AF:
0.336
Hom.:
1148
Bravo
AF:
0.297
Asia WGS
AF:
0.234
AC:
815
AN:
3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.96
CADD
Benign
8.2
DANN
Benign
0.68

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: rs4943110; hg19: chr13-34035860; API