8-38143305-AT-A

Position:

• chr8-38143305-AT-A

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_Moderate BA1

The NM_000349.3(STAR):​c.*967del 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

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

Verdict is Benign. Variant got -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/exons	MANE	UniProt
STAR	NM_000349.3	c.*967del		3_prime_UTR_variant	7/7	ENST00000276449.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
STAR	ENST00000276449.9	c.*967del		3_prime_UTR_variant	7/7	1	NM_000349.3	P1
ASH2L	ENST00000521808.5	c.*5-415del		intron_variant		5

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

Gnomad4 AFR AF: 0.698

Gnomad4 AMR AF: 0.816

Gnomad4 ASJ AF: 0.900

Gnomad4 EAS AF: 0.683

Gnomad4 SAS AF: 0.843

Gnomad4 FIN AF: 0.814

Gnomad4 NFE AF: 0.900

Gnomad4 OTH AF: 0.837

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

Congenital adrenal hyperplasia Benign:1

Benign, criteria provided, single submitter

clinical testing

Illumina Laboratory Services, Illumina

Jun 14, 2016

- -

Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11326306; hg19: chr8-38000823;