8-38143305-AT-A

Variant names:

• chr8-38143305-AT-A
• rs11326306
• NM_000349.3:c.*967delA

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP6_Moderate BA1

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

• Frequency: Genomes: 𝑓 0.82 (35765 hom., cov: 0)
• Consequence: STAR NM_000349.3 3_prime_UTR
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -1.97
• Publications: 0 publications found

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]

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]

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP6: Variant 8-38143305-AT-A is Benign according to our data. Variant chr8-38143305-AT-A is described in ClinVar as [Benign]. Clinvar id is 362832.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.893 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
STAR	NM_000349.3	c.*967delA		3_prime_UTR_variant	Exon 7 of 7	ENST00000276449.9	NP_000340.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
STAR	ENST00000276449.9	c.*967delA		3_prime_UTR_variant	Exon 7 of 7	1	NM_000349.3	ENSP00000276449.3
ASH2L	ENST00000521808.5	c.*5-415delT		intron_variant	Intron 3 of 3	5		ENSP00000427839.1

Frequencies

GnomAD3 genomes AF: 0.821 AC: 87917 AN: 107118 Hom.: 35795 Cov.: 0

Gnomad AFR AF: 0.699

Gnomad AMI AF: 0.920

Gnomad AMR AF: 0.817

Gnomad ASJ AF: 0.900

Gnomad EAS AF: 0.683

Gnomad SAS AF: 0.844

Gnomad FIN AF: 0.814

Gnomad MID AF: 0.910

Gnomad NFE AF: 0.900

Gnomad OTH AF: 0.839

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

GnomAD4 genome AF: 0.820 AC: 87881 AN: 107132 Hom.: 35765 Cov.: 0 AF XY: 0.818 AC XY: 41708 AN XY: 50972

African (AFR) AF: 0.698 AC: 20943 AN: 30002

American (AMR) AF: 0.816 AC: 8529 AN: 10448

Ashkenazi Jewish (ASJ) AF: 0.900 AC: 2316 AN: 2572

East Asian (EAS) AF: 0.683 AC: 2680 AN: 3924

South Asian (SAS) AF: 0.843 AC: 2695 AN: 3196

European-Finnish (FIN) AF: 0.814 AC: 4733 AN: 5816

Middle Eastern (MID) AF: 0.911 AC: 195 AN: 214

European-Non Finnish (NFE) AF: 0.900 AC: 43948 AN: 48830

Other (OTH) AF: 0.837 AC: 1189 AN: 1420

Alfa AF: 0.710 Hom.: 1101

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

Congenital adrenal hyperplasia Benign:1

Jun 14, 2016

Illumina Laboratory Services, Illumina

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

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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

Other links and lift over

dbSNP: rs11326306; hg19: chr8-38000823;