rs538874

Positions:

• chr13-33115601-G-A
• chr13-33115601-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000336934.10(STARD13):​c.2281+2464C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.227 in 152,048 control chromosomes in the GnomAD database, including 4,209 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 0.23 (4209 hom., cov: 32)
• Consequence: STARD13 ENST00000336934.10 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.758

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.303 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
STARD13	NM_178006.4	c.2281+2464C>T		intron_variant		ENST00000336934.10	NP_821074.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
STARD13	ENST00000336934.10	c.2281+2464C>T		intron_variant		1	NM_178006.4	ENSP00000338785	P4
STARD13	ENST00000255486.8	c.2257+2464C>T		intron_variant		1		ENSP00000255486	A2
STARD13	ENST00000399365.7	c.1927+2464C>T		intron_variant		1		ENSP00000382300
STARD13	ENST00000567873.2	c.2236+2464C>T		intron_variant		1		ENSP00000456233	A2

Frequencies

GnomAD3 genomes AF: 0.227 AC: 34543 AN: 151930 Hom.: 4198 Cov.: 32

Gnomad AFR AF: 0.298

Gnomad AMI AF: 0.207

Gnomad AMR AF: 0.185

Gnomad ASJ AF: 0.158

Gnomad EAS AF: 0.316

Gnomad SAS AF: 0.185

Gnomad FIN AF: 0.148

Gnomad MID AF: 0.231

Gnomad NFE AF: 0.206

Gnomad OTH AF: 0.220

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

GnomAD4 genome AF: 0.227 AC: 34587 AN: 152048 Hom.: 4209 Cov.: 32 AF XY: 0.223 AC XY: 16568 AN XY: 74340

Gnomad4 AFR AF: 0.298

Gnomad4 AMR AF: 0.185

Gnomad4 ASJ AF: 0.158

Gnomad4 EAS AF: 0.315

Gnomad4 SAS AF: 0.185

Gnomad4 FIN AF: 0.148

Gnomad4 NFE AF: 0.206

Gnomad4 OTH AF: 0.228

Alfa AF: 0.204 Hom.: 1761

Bravo AF: 0.232

Asia WGS AF: 0.289 AC: 1003 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.16
DANN	Benign	0.57

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

Other links and lift over

dbSNP: rs538874; hg19: chr13-33689738;