Genetic Variant STAR:c.*965_*967dupAAA (chr8-38143305-A-ATTT) – ACMG Classification: Uncertain_significance (0 pts)

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 0P and 0B.

The NM_000349.3(STAR):c.*965_*967dupAAA variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: 𝑓 0.033 ( 185 hom., cov: 0)

Failed GnomAD Quality Control

Consequence

STAR
NM_000349.3 3_prime_UTR

Scores

Not classified

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: -1.97

Publications

0 publications found

Variant links:

Genes affected

STAR (HGNC:11359): (steroidogenic acute regulatory protein) The protein encoded by this gene plays a key role in the acute regulation of steroid hormone synthesis by enhancing the conversion of cholesterol into pregnenolone. This protein permits the cleavage of cholesterol into pregnenolone by mediating the transport of cholesterol from the outer mitochondrial membrane to the inner mitochondrial membrane. Mutations in this gene are a cause of congenital lipoid adrenal hyperplasia (CLAH), also called lipoid CAH. A pseudogene of this gene is located on chromosome 13. [provided by RefSeq, Jul 2008]

STAR links:

ASH2L (HGNC:744): (ASH2 like, histone lysine methyltransferase complex subunit) Enables beta-catenin binding activity and transcription cis-regulatory region binding activity. Contributes to histone methyltransferase activity (H3-K4 specific). Involved in histone H3-K4 methylation; positive regulation of cell population proliferation; and response to estrogen. Acts upstream of or within cellular response to DNA damage stimulus. Located in nucleus. Part of MLL3/4 complex and Set1C/COMPASS complex. [provided by Alliance of Genome Resources, Apr 2022]

ASH2L links:

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ACMG classification

Classification was made for transcript

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
STAR	NM_000349.3 link	c.965_967dupAAA		3_prime_UTR_variant	Exon 7 of 7	ENST00000276449.9	NP_000340.2	P49675Q6IBK0

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
STAR	ENST00000276449.9 link	c.965_967dupAAA		3_prime_UTR_variant	Exon 7 of 7	1	NM_000349.3	ENSP00000276449.3		P49675
ASH2L	ENST00000521808.5 link	c.5-417_5-415dupTTT		intron_variant	Intron 3 of 3	5		ENSP00000427839.1		H0YAQ0

Frequencies

GnomAD3 genomes

AF:

0.0331

AC:

3547

AN:

107150

Hom.:

185

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0273

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0819

Gnomad ASJ

AF:

0.00233

Gnomad EAS

AF:

0.260

Gnomad SAS

AF:

0.0252

Gnomad FIN

AF:

0.0809

Gnomad MID

AF:

0.0214

Gnomad NFE

AF:

0.00493

Gnomad OTH

AF:

0.0303

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

GnomAD4 genome

Data not reliable, filtered out with message: AS_VQSR

AF:

0.0331

AC:

3552

AN:

107164

Hom.:

185

Cov.:

AF XY:

0.0386

AC XY:

1969

AN XY:

50984

show subpopulations

African (AFR)

AF:

0.0273

AC:

822

AN:

30072

American (AMR)

AF:

0.0823

AC:

860

AN:

10444

Ashkenazi Jewish (ASJ)

AF:

0.00233

AC:

AN:

2572

East Asian (EAS)

AF:

0.260

AC:

1028

AN:

3950

South Asian (SAS)

AF:

0.0253

AC:

AN:

3196

European-Finnish (FIN)

AF:

0.0809

AC:

465

AN:

5748

Middle Eastern (MID)

AF:

0.0234

AC:

AN:

214

European-Non Finnish (NFE)

AF:

0.00493

AC:

241

AN:

48838

Other (OTH)

AF:

0.0310

AC:

AN:

1420

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.516

Heterozygous variant carriers

121

242

362

483

604

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Alfa

AF:

0.0240

Hom.:

1101

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

Congenital adrenal hyperplasia

Uncertain:1

Jun 14, 2016

Illumina Laboratory Services, Illumina

Significance:Uncertain significance

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

PhyloP100

-2.0

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

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8-38143305-A-ATTT

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

Other links and lift over