Variant chr2-190208668-A-ATT 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+212insAA variant causes a intron change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.25 ( 4546 hom., cov: 0)

Exomes 𝑓: 0.14 ( 381 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:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP6

Variant 2-190208668-A-ATT is Benign according to our data. Variant chr2-190208668-A-ATT is described in ClinVar as [Benign]. Clinvar id is 1265562.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.313 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+212insAA		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+212insAA		intron_variant		1	NM_014362.4	P1	Q6NVY1-1

Frequencies

GnomAD3 genomes

AF:

0.253

AC:

34402

AN:

136092

Hom.:

4543

Cov.:

show subpopulations

Gnomad AFR

AF:

0.318

Gnomad AMI

AF:

0.184

Gnomad AMR

AF:

0.259

Gnomad ASJ

AF:

0.217

Gnomad EAS

AF:

0.316

Gnomad SAS

AF:

0.179

Gnomad FIN

AF:

0.108

Gnomad MID

AF:

0.323

Gnomad NFE

AF:

0.233

Gnomad OTH

AF:

0.269

GnomAD4 exome

AF:

0.135

AC:

43331

AN:

320614

Hom.:

381

Cov.:

AF XY:

0.134

AC XY:

22996

AN XY:

171664

show subpopulations

Gnomad4 AFR exome

AF:

0.198

Gnomad4 AMR exome

AF:

0.129

Gnomad4 ASJ exome

AF:

0.115

Gnomad4 EAS exome

AF:

0.203

Gnomad4 SAS exome

AF:

0.124

Gnomad4 FIN exome

AF:

0.0859

Gnomad4 NFE exome

AF:

0.135

Gnomad4 OTH exome

AF:

0.130

GnomAD4 genome

AF:

0.253

AC:

34409

AN:

136098

Hom.:

4546

Cov.:

AF XY:

0.247

AC XY:

16240

AN XY:

65656

show subpopulations

Gnomad4 AFR

AF:

0.318

Gnomad4 AMR

AF:

0.259

Gnomad4 ASJ

AF:

0.217

Gnomad4 EAS

AF:

0.316

Gnomad4 SAS

AF:

0.180

Gnomad4 FIN

AF:

0.108

Gnomad4 NFE

AF:

0.233

Gnomad4 OTH

AF:

0.271

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 13, 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