15-42656664-A-G

Position:

• chr15-42656664-A-G

Variant summary

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

The NM_020759.3(STARD9):​c.702+4072A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.415 in 152,080 control chromosomes in the GnomAD database, including 18,789 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 0.42 (18789 hom., cov: 31)
• Consequence: STARD9 NM_020759.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.803

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]

STARD9 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.835 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
STARD9	NM_020759.3	c.702+4072A>G		intron_variant		ENST00000290607.12	NP_065810.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
STARD9	ENST00000290607.12	c.702+4072A>G		intron_variant		5	NM_020759.3	ENSP00000290607.7
STARD9	ENST00000564158.5	n.759+4072A>G		intron_variant		1
STARD9	ENST00000568493.1	n.773+4072A>G		intron_variant		2

Frequencies

GnomAD3 genomes AF: 0.415 AC: 63066 AN: 151962 Hom.: 18729 Cov.: 31

Gnomad AFR AF: 0.842

Gnomad AMI AF: 0.0934

Gnomad AMR AF: 0.289

Gnomad ASJ AF: 0.325

Gnomad EAS AF: 0.289

Gnomad SAS AF: 0.457

Gnomad FIN AF: 0.255

Gnomad MID AF: 0.275

Gnomad NFE AF: 0.226

Gnomad OTH AF: 0.368

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

GnomAD4 genome AF: 0.415 AC: 63182 AN: 152080 Hom.: 18789 Cov.: 31 AF XY: 0.413 AC XY: 30715 AN XY: 74332

Gnomad4 AFR AF: 0.842

Gnomad4 AMR AF: 0.289

Gnomad4 ASJ AF: 0.325

Gnomad4 EAS AF: 0.290

Gnomad4 SAS AF: 0.457

Gnomad4 FIN AF: 0.255

Gnomad4 NFE AF: 0.226

Gnomad4 OTH AF: 0.364

Alfa AF: 0.246 Hom.: 7609

Bravo AF: 0.435

Asia WGS AF: 0.413 AC: 1438 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.34
DANN	Benign	0.44

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: rs8043472; hg19: chr15-42948862;