chr15-42696214-C-A

Position:

• chr15-42696214-C-A

Variant summary

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

The NM_020759.3(STARD9):​c.13284+334C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.388 in 152,124 control chromosomes in the GnomAD database, including 17,532 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 0.39 (17532 hom., cov: 33)
• Consequence: STARD9 NM_020759.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.379

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=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.826 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
STARD9	NM_020759.3	c.13284+334C>A		intron_variant		ENST00000290607.12	NP_065810.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
STARD9	ENST00000290607.12	c.13284+334C>A		intron_variant		5	NM_020759.3	ENSP00000290607.7
STARD9	ENST00000562619.1	n.*575+334C>A		intron_variant		1		ENSP00000454648.1

Frequencies

GnomAD3 genomes AF: 0.388 AC: 58910 AN: 152006 Hom.: 17476 Cov.: 33

Gnomad AFR AF: 0.833

Gnomad AMI AF: 0.0921

Gnomad AMR AF: 0.198

Gnomad ASJ AF: 0.305

Gnomad EAS AF: 0.230

Gnomad SAS AF: 0.426

Gnomad FIN AF: 0.236

Gnomad MID AF: 0.250

Gnomad NFE AF: 0.202

Gnomad OTH AF: 0.334

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

GnomAD4 genome AF: 0.388 AC: 59022 AN: 152124 Hom.: 17532 Cov.: 33 AF XY: 0.385 AC XY: 28600 AN XY: 74342

Gnomad4 AFR AF: 0.833

Gnomad4 AMR AF: 0.198

Gnomad4 ASJ AF: 0.305

Gnomad4 EAS AF: 0.231

Gnomad4 SAS AF: 0.426

Gnomad4 FIN AF: 0.236

Gnomad4 NFE AF: 0.202

Gnomad4 OTH AF: 0.331

Alfa AF: 0.218 Hom.: 2151

Bravo AF: 0.398

Asia WGS AF: 0.350 AC: 1218 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	7.3
DANN	Benign	0.55

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: rs6493061; hg19: chr15-42988412;