rs6493061

Variant names:

• chr15-42696214-C-A
• rs6493061
• NM_020759.3:c.13284+334C>A

Your query was ambiguous. Multiple possible variants found:

• chr15-42696214-C-A
• chr15-42696214-C-G
• chr15-42696214-C-T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 4 publications found

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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
STARD9	NM_020759.3	c.13284+334C>A		intron_variant	Intron 26 of 32	ENST00000290607.12	NP_065810.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
STARD9	ENST00000290607.12	c.13284+334C>A		intron_variant	Intron 26 of 32	5	NM_020759.3	ENSP00000290607.7
STARD9	ENST00000562619.1	n.*575+334C>A		intron_variant	Intron 4 of 9	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

African (AFR) AF: 0.833 AC: 34589 AN: 41510

American (AMR) AF: 0.198 AC: 3021 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.305 AC: 1057 AN: 3470

East Asian (EAS) AF: 0.231 AC: 1196 AN: 5180

South Asian (SAS) AF: 0.426 AC: 2050 AN: 4816

European-Finnish (FIN) AF: 0.236 AC: 2495 AN: 10554

Middle Eastern (MID) AF: 0.262 AC: 77 AN: 294

European-Non Finnish (NFE) AF: 0.202 AC: 13754 AN: 67990

Other (OTH) AF: 0.331 AC: 699 AN: 2114

Alfa AF: 0.226 Hom.: 2666

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
PhyloP100		0.38
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: rs6493061; hg19: chr15-42988412;