Variant X-119565357-A-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBP6_Very_Strong

The NM_022101.4(STEEP1):c.-2T>C variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.90 ( 31653 hom., 28777 hem., cov: 22)

Exomes 𝑓: 0.87 ( 274868 hom. 308434 hem. )

Failed GnomAD Quality Control

Consequence

STEEP1
NM_022101.4 5_prime_UTR

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -0.586

Variant links:

Genes affected

STEEP1 (HGNC:26239): (STING1 ER exit protein 1) While this gene is well-supported by transcript data, no functional information on its protein products is currently available. Three transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Dec 2009]

STEEP1 links:

UBE2A (HGNC:12472): (ubiquitin conjugating enzyme E2 A) The modification of proteins with ubiquitin is an important cellular mechanism for targeting abnormal or short-lived proteins for degradation. Ubiquitination involves at least three classes of enzymes: ubiquitin-activating enzymes, ubiquitin-conjugating enzymes, and ubiquitin-protein ligases. This gene encodes a member of the E2 ubiquitin-conjugating enzyme family. This enzyme is required for post-replicative DNA damage repair, and may play a role in transcriptional regulation. Mutations in this gene are associated with cognitive disability. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Aug 2013]

UBE2A links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.72).

BP6

Variant X-119565357-A-G is Benign according to our data. Variant chrX-119565357-A-G is described in ClinVar as [Benign]. Clinvar id is 1255438.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	#exon/exons	MANE	Protein	UniProt
STEEP1	NM_022101.4 linkuse as main transcript	c.-2T>C	5_prime_UTR_variant	1/7	ENST00000644802.2	NP_071384.1	Q9H5V9-1
STEEP1	NM_001170570.2 linkuse as main transcript	c.-2T>C	5_prime_UTR_variant	1/6		NP_001164041.1	Q9H5V9-3
STEEP1	NM_001170569.1 linkuse as main transcript	c.-256T>C	5_prime_UTR_variant	1/7		NP_001164040.1	Q9H5V9-2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
STEEP1	ENST00000644802.2 linkuse as main transcript	c.-2T>C		5_prime_UTR_variant	1/7		NM_022101.4	ENSP00000494123.2		Q9H5V9-1

Frequencies

GnomAD3 genomes

AF:

0.899

AC:

98694

AN:

109782

Hom.:

31655

Cov.:

AF XY:

0.898

AC XY:

28712

AN XY:

31982

show subpopulations

Gnomad AFR

AF:

0.981

Gnomad AMI

AF:

0.943

Gnomad AMR

AF:

0.934

Gnomad ASJ

AF:

0.881

Gnomad EAS

AF:

0.999

Gnomad SAS

AF:

0.946

Gnomad FIN

AF:

0.792

Gnomad MID

AF:

0.865

Gnomad NFE

AF:

0.848

Gnomad OTH

AF:

0.902

GnomAD3 exomes

AF:

0.892

AC:

157450

AN:

176430

Hom.:

46271

AF XY:

0.889

AC XY:

54473

AN XY:

61296

show subpopulations

Gnomad AFR exome

AF:

0.983

Gnomad AMR exome

AF:

0.957

Gnomad ASJ exome

AF:

0.870

Gnomad EAS exome

AF:

1.00

Gnomad SAS exome

AF:

0.938

Gnomad FIN exome

AF:

0.797

Gnomad NFE exome

AF:

0.850

Gnomad OTH exome

AF:

0.887

GnomAD4 exome

Data not reliable, filtered out with message: AS_VQSR;InbreedingCoeff

AF:

0.866

AC:

942641

AN:

1088202

Hom.:

274868

Cov.:

AF XY:

0.870

AC XY:

308434

AN XY:

354482

show subpopulations

Gnomad4 AFR exome

AF:

0.984

Gnomad4 AMR exome

AF:

0.956

Gnomad4 ASJ exome

AF:

0.869

Gnomad4 EAS exome

AF:

1.00

Gnomad4 SAS exome

AF:

0.936

Gnomad4 FIN exome

AF:

0.797

Gnomad4 NFE exome

AF:

0.852

Gnomad4 OTH exome

AF:

0.887

GnomAD4 genome

Data not reliable, filtered out with message: InbreedingCoeff

AF:

0.899

AC:

98752

AN:

109834

Hom.:

31653

Cov.:

AF XY:

0.898

AC XY:

28777

AN XY:

32044

show subpopulations

Gnomad4 AFR

AF:

0.981

Gnomad4 AMR

AF:

0.934

Gnomad4 ASJ

AF:

0.881

Gnomad4 EAS

AF:

0.999

Gnomad4 SAS

AF:

0.946

Gnomad4 FIN

AF:

0.792

Gnomad4 NFE

AF:

0.848

Gnomad4 OTH

AF:

0.904

Alfa

AF:

0.867

Hom.:

73809

Bravo

AF:

0.915

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

Intellectual disability, X-linked 107

Benign:1

Benign, criteria provided, single submitter

clinical testing

Genome-Nilou Lab

Jul 30, 2021

- -

not provided

Benign:1

Benign, criteria provided, single submitter

not provided

Breakthrough Genomics, Breakthrough Genomics

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.72

CADD

Benign

6.4

DANN

Benign

0.65

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over