Genetic Variant ENST00000653421.2:n.1580T>C (chr13-33633563-A-G) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000653421.2(ENSG00000230490):n.1580T>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.108 in 152,276 control chromosomes in the GnomAD database, including 1,451 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 0.11 ( 1451 hom., cov: 33)

Consequence

ENSG00000230490
ENST00000653421.2 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.22

Publications

4 publications found

Variant links:

Genes affected

ENSG00000230490 (HGNC:):

ENSG00000230490 links:

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]

STARD13 Gene-Disease associations (from GenCC):

schizophrenia
Inheritance: Unknown Classification: NO_KNOWN Submitted by: Labcorp Genetics (formerly Invitae)

STARD13 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

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

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.8).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.225 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
STARD13	NM_001243476.3 link	c.-106+27714T>C		intron_variant	Intron 3 of 17		NP_001230405.1	Q9Y3M8
STARD13	XM_017020835.3 link	c.-106+43115T>C		intron_variant	Intron 1 of 15		XP_016876324.1

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
ENSG00000230490	ENST00000653421.2 link	n.1580T>C	non_coding_transcript_exon_variant	Exon 2 of 2
ENSG00000230490	ENST00000730909.1 link	n.1661T>C	non_coding_transcript_exon_variant	Exon 3 of 3
ENSG00000230490	ENST00000730910.1 link	n.1719T>C	non_coding_transcript_exon_variant	Exon 4 of 4

Frequencies

GnomAD3 genomes

AF:

0.107

AC:

16309

AN:

152158

Hom.:

1436

Cov.:

show subpopulations

Gnomad AFR

AF:

0.228

Gnomad AMI

AF:

0.00219

Gnomad AMR

AF:

0.138

Gnomad ASJ

AF:

0.0412

Gnomad EAS

AF:

0.184

Gnomad SAS

AF:

0.0197

Gnomad FIN

AF:

0.0818

Gnomad MID

AF:

0.0696

Gnomad NFE

AF:

0.0361

Gnomad OTH

AF:

0.0975

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

GnomAD4 genome

AF:

0.108

AC:

16378

AN:

152276

Hom.:

1451

Cov.:

AF XY:

0.109

AC XY:

8140

AN XY:

74460

show subpopulations

African (AFR)

AF:

0.229

AC:

9516

AN:

41538

American (AMR)

AF:

0.139

AC:

2121

AN:

15290

Ashkenazi Jewish (ASJ)

AF:

0.0412

AC:

143

AN:

3470

East Asian (EAS)

AF:

0.184

AC:

953

AN:

5184

South Asian (SAS)

AF:

0.0193

AC:

AN:

4830

European-Finnish (FIN)

AF:

0.0818

AC:

868

AN:

10606

Middle Eastern (MID)

AF:

0.0748

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0361

AC:

2457

AN:

68038

Other (OTH)

AF:

0.0960

AC:

203

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

704

1408

2111

2815

3519

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

164

328

492

656

820

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.0610

Hom.:

2206

Bravo

AF:

0.119

Asia WGS

AF:

0.116

AC:

403

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.80

CADD

Benign

2.1

(source)

DANN

Benign

0.67

PhyloP100

1.2

Splicing

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over