chr13-33119700-C-T

Variant names:

• chr13-33119700-C-T
• rs9315204
• NM_178006.4:c.2083-1437G>A

Variant summary

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

The NM_178006.4(STARD13):​c.2083-1437G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.205 in 152,102 control chromosomes in the GnomAD database, including 3,584 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 0.20 (3584 hom., cov: 33)
• Consequence: STARD13 NM_178006.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.152
• Publications: 38 publications found

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]

STARD13 Gene-Disease associations (from GenCC):

• schizophrenia

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

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.282 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
STARD13	NM_178006.4	c.2083-1437G>A		intron_variant	Intron 7 of 13	ENST00000336934.10	NP_821074.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
STARD13	ENST00000336934.10	c.2083-1437G>A		intron_variant	Intron 7 of 13	1	NM_178006.4	ENSP00000338785.4
STARD13	ENST00000255486.8	c.2059-1437G>A		intron_variant	Intron 7 of 13	1		ENSP00000255486.4
STARD13	ENST00000567873.2	c.2038-1437G>A		intron_variant	Intron 7 of 13	1		ENSP00000456233.2
STARD13	ENST00000399365.7	c.1729-1437G>A		intron_variant	Intron 7 of 13	1		ENSP00000382300.3

Frequencies

GnomAD3 genomes AF: 0.205 AC: 31151 AN: 151984 Hom.: 3579 Cov.: 33

Gnomad AFR AF: 0.115

Gnomad AMI AF: 0.140

Gnomad AMR AF: 0.262

Gnomad ASJ AF: 0.157

Gnomad EAS AF: 0.222

Gnomad SAS AF: 0.296

Gnomad FIN AF: 0.344

Gnomad MID AF: 0.117

Gnomad NFE AF: 0.221

Gnomad OTH AF: 0.201

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

GnomAD4 genome AF: 0.205 AC: 31160 AN: 152102 Hom.: 3584 Cov.: 33 AF XY: 0.213 AC XY: 15836 AN XY: 74344

African (AFR) AF: 0.115 AC: 4766 AN: 41494

American (AMR) AF: 0.262 AC: 4008 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.157 AC: 544 AN: 3472

East Asian (EAS) AF: 0.223 AC: 1151 AN: 5172

South Asian (SAS) AF: 0.294 AC: 1416 AN: 4810

European-Finnish (FIN) AF: 0.344 AC: 3637 AN: 10574

Middle Eastern (MID) AF: 0.119 AC: 35 AN: 294

European-Non Finnish (NFE) AF: 0.221 AC: 15056 AN: 67982

Other (OTH) AF: 0.199 AC: 419 AN: 2110

Alfa AF: 0.214 Hom.: 12904

Bravo AF: 0.195

Asia WGS AF: 0.241 AC: 840 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	8.4
DANN	Benign	0.55
PhyloP100		0.15
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs9315204; hg19: chr13-33693837;