rs3199486

Positions:

• chr15-42719997-T-C
• chr15-42719997-T-G

Variant summary

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

The NM_020759.3(STARD9):​c.*423T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.391 in 165,114 control chromosomes in the GnomAD database, including 18,741 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 0.40 (18202 hom., cov: 32)
  • Exomes 𝑓: 0.26 (539 hom.)
• Consequence: STARD9 NM_020759.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.120

Genes affected

STARD9 (HGNC:19162): (StAR related lipid transfer domain containing 9) Enables microtubule binding activity and microtubule motor activity. Involved in spindle assembly. Located in centriole; cytoplasm; and nucleus. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.73).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.832 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
STARD9	NM_020759.3	c.*423T>C		3_prime_UTR_variant	33/33	ENST00000290607.12	NP_065810.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
STARD9	ENST00000290607.12	c.*423T>C		3_prime_UTR_variant	33/33	5	NM_020759.3	ENSP00000290607	P1
STARD9	ENST00000562619.1	c.*1614T>C		3_prime_UTR_variant, NMD_transcript_variant	10/10	1		ENSP00000454648

Frequencies

GnomAD3 genomes AF: 0.402 AC: 61128 AN: 152038 Hom.: 18142 Cov.: 32

Gnomad AFR AF: 0.839

Gnomad AMI AF: 0.0934

Gnomad AMR AF: 0.219

Gnomad ASJ AF: 0.330

Gnomad EAS AF: 0.246

Gnomad SAS AF: 0.424

Gnomad FIN AF: 0.249

Gnomad MID AF: 0.272

Gnomad NFE AF: 0.221

Gnomad OTH AF: 0.352

GnomAD4 exome AF: 0.260 AC: 3369 AN: 12958 Hom.: 539 Cov.: 0 AF XY: 0.264 AC XY: 1719 AN XY: 6510

Gnomad4 AFR exome AF: 0.835

Gnomad4 AMR exome AF: 0.185

Gnomad4 ASJ exome AF: 0.355

Gnomad4 EAS exome AF: 0.228

Gnomad4 SAS exome AF: 0.400

Gnomad4 FIN exome AF: 0.245

Gnomad4 NFE exome AF: 0.227

Gnomad4 OTH exome AF: 0.284

GnomAD4 genome AF: 0.403 AC: 61244 AN: 152156 Hom.: 18202 Cov.: 32 AF XY: 0.399 AC XY: 29683 AN XY: 74376

Gnomad4 AFR AF: 0.840

Gnomad4 AMR AF: 0.219

Gnomad4 ASJ AF: 0.330

Gnomad4 EAS AF: 0.247

Gnomad4 SAS AF: 0.423

Gnomad4 FIN AF: 0.249

Gnomad4 NFE AF: 0.221

Gnomad4 OTH AF: 0.348

Alfa AF: 0.244 Hom.: 8907

Bravo AF: 0.415

Asia WGS AF: 0.355 AC: 1236 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.73
CADD	Benign	10
DANN	Benign	0.73

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: rs3199486; hg19: chr15-43012195;