chr13-33224125-A-C

Variant names:

• chr13-33224125-A-C
• rs2555603
• NM_178006.4:c.170-56503T>G

Variant summary

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

The NM_178006.4(STARD13):​c.170-56503T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.211 in 152,132 control chromosomes in the GnomAD database, including 3,719 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 0.21 (3719 hom., cov: 32)
• Consequence: STARD13 NM_178006.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.206
• Publications: 11 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-AS (HGNC:40873): (STARD13 antisense RNA)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.297 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
STARD13	NM_178006.4	c.170-56503T>G		intron_variant	Intron 1 of 13	ENST00000336934.10	NP_821074.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
STARD13	ENST00000336934.10	c.170-56503T>G		intron_variant	Intron 1 of 13	1	NM_178006.4	ENSP00000338785.4

Frequencies

GnomAD3 genomes AF: 0.211 AC: 32077 AN: 152014 Hom.: 3714 Cov.: 32

Gnomad AFR AF: 0.122

Gnomad AMI AF: 0.216

Gnomad AMR AF: 0.166

Gnomad ASJ AF: 0.282

Gnomad EAS AF: 0.161

Gnomad SAS AF: 0.309

Gnomad FIN AF: 0.290

Gnomad MID AF: 0.278

Gnomad NFE AF: 0.256

Gnomad OTH AF: 0.222

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

GnomAD4 genome AF: 0.211 AC: 32085 AN: 152132 Hom.: 3719 Cov.: 32 AF XY: 0.213 AC XY: 15843 AN XY: 74362

African (AFR) AF: 0.122 AC: 5069 AN: 41532

American (AMR) AF: 0.165 AC: 2525 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.282 AC: 979 AN: 3472

East Asian (EAS) AF: 0.161 AC: 834 AN: 5170

South Asian (SAS) AF: 0.310 AC: 1496 AN: 4826

European-Finnish (FIN) AF: 0.290 AC: 3059 AN: 10564

Middle Eastern (MID) AF: 0.269 AC: 79 AN: 294

European-Non Finnish (NFE) AF: 0.256 AC: 17381 AN: 67970

Other (OTH) AF: 0.221 AC: 466 AN: 2108

Alfa AF: 0.237 Hom.: 20276

Bravo AF: 0.197

Asia WGS AF: 0.210 AC: 732 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.8
DANN	Benign	0.76
PhyloP100		0.21
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: rs2555603; hg19: chr13-33798262;