15-42719997-T-C

Variant names:

• chr15-42719997-T-C
• rs3199486
• ENST00000562619.1:n.*1614T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000562619.1(STARD9):​n.*1614T>C variant causes a non coding transcript exon 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 ENST00000562619.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.120
• Publications: 5 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=-0.73).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.832 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000562619.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	STARD9	NM_020759.3	MANE Select	c.*423T>C		3_prime_UTR	Exon 33 of 33	NP_065810.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	STARD9	ENST00000562619.1	TSL:1	n.*1614T>C		non_coding_transcript_exon	Exon 10 of 10	ENSP00000454648.1
	STARD9	ENST00000290607.12	TSL:5 MANE Select	c.*423T>C		3_prime_UTR	Exon 33 of 33	ENSP00000290607.7
	STARD9	ENST00000562619.1	TSL:1	n.*1614T>C		3_prime_UTR	Exon 10 of 10	ENSP00000454648.1

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

African (AFR) AF: 0.835 AC: 319 AN: 382

American (AMR) AF: 0.185 AC: 185 AN: 1000

Ashkenazi Jewish (ASJ) AF: 0.355 AC: 150 AN: 422

East Asian (EAS) AF: 0.228 AC: 94 AN: 412

South Asian (SAS) AF: 0.400 AC: 284 AN: 710

European-Finnish (FIN) AF: 0.245 AC: 118 AN: 482

Middle Eastern (MID) AF: 0.352 AC: 19 AN: 54

European-Non Finnish (NFE) AF: 0.227 AC: 1967 AN: 8676

Other (OTH) AF: 0.284 AC: 233 AN: 820

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

African (AFR) AF: 0.840 AC: 34848 AN: 41506

American (AMR) AF: 0.219 AC: 3349 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.330 AC: 1145 AN: 3472

East Asian (EAS) AF: 0.247 AC: 1277 AN: 5180

South Asian (SAS) AF: 0.423 AC: 2041 AN: 4824

European-Finnish (FIN) AF: 0.249 AC: 2635 AN: 10590

Middle Eastern (MID) AF: 0.286 AC: 84 AN: 294

European-Non Finnish (NFE) AF: 0.221 AC: 15046 AN: 67982

Other (OTH) AF: 0.348 AC: 734 AN: 2110

Alfa AF: 0.261 Hom.: 16325

Bravo AF: 0.415

Asia WGS AF: 0.355 AC: 1236 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.73
CADD	Benign	10
DANN	Benign	0.73
PhyloP100		-0.12
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: rs3199486; hg19: chr15-43012195;