Variant chr2-190208668-A-ATTTT details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBA1

The NM_014362.4(HIBCH):c.1045+211_1045+212insAAAA variant causes a intron change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.017 ( 83 hom., cov: 0)

Exomes 𝑓: 0.0032 ( 2 hom. )

Consequence

HIBCH
NM_014362.4 intron

Scores

Not classified

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.641

Variant links:

Genes affected

HIBCH (HGNC:4908): (3-hydroxyisobutyryl-CoA hydrolase) This gene encodes the enzyme responsible for hydrolysis of both HIBYL-CoA and beta-hydroxypropionyl-CoA. Mutations in this gene have been associated with 3-hyroxyisobutyryl-CoA hydrolase deficiency. Alternative splicing results in multiple transcript variants.[provided by RefSeq, May 2010]

HIBCH links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP6

Variant 2-190208668-A-ATTTT is Benign according to our data. Variant chr2-190208668-A-ATTTT is described in ClinVar as [Benign]. Clinvar id is 1279360.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0575 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
HIBCH	NM_014362.4 linkuse as main transcript	c.1045+211_1045+212insAAAA		intron_variant		ENST00000359678.10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
HIBCH	ENST00000359678.10 linkuse as main transcript	c.1045+211_1045+212insAAAA		intron_variant		1	NM_014362.4	P1	Q6NVY1-1

Frequencies

GnomAD3 genomes

AF:

0.0172

AC:

2343

AN:

136296

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0595

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00820

Gnomad ASJ

AF:

0.000313

Gnomad EAS

AF:

0.00105

Gnomad SAS

AF:

0.000232

Gnomad FIN

AF:

0.000133

Gnomad MID

AF:

0.00347

Gnomad NFE

AF:

0.000285

Gnomad OTH

AF:

0.0145

GnomAD4 exome

AF:

0.00323

AC:

1055

AN:

326654

Hom.:

Cov.:

AF XY:

0.00334

AC XY:

584

AN XY:

174878

show subpopulations

Gnomad4 AFR exome

AF:

0.0230

Gnomad4 AMR exome

AF:

0.00279

Gnomad4 ASJ exome

AF:

0.00123

Gnomad4 EAS exome

AF:

0.0101

Gnomad4 SAS exome

AF:

0.00459

Gnomad4 FIN exome

AF:

0.000835

Gnomad4 NFE exome

AF:

0.00183

Gnomad4 OTH exome

AF:

0.00398

GnomAD4 genome

AF:

0.0172

AC:

2348

AN:

136304

Hom.:

Cov.:

AF XY:

0.0173

AC XY:

1139

AN XY:

65786

show subpopulations

Gnomad4 AFR

AF:

0.0596

Gnomad4 AMR

AF:

0.00819

Gnomad4 ASJ

AF:

0.000313

Gnomad4 EAS

AF:

0.00105

Gnomad4 SAS

AF:

0.000233

Gnomad4 FIN

AF:

0.000133

Gnomad4 NFE

AF:

0.000285

Gnomad4 OTH

AF:

0.0144

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

May 18, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

Splicing

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