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

Frequency

Genomes: 𝑓 0.046 ( 178 hom., cov: 0)

Exomes 𝑓: 0.14 ( 45 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-AT is Benign according to our data. Variant chr2-190208668-A-AT is described in ClinVar as [Benign]. Clinvar id is 1287537.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0703 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+212insA		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+212insA		intron_variant		1	NM_014362.4	P1	Q6NVY1-1

Frequencies

GnomAD3 genomes

AF:

0.0459

AC:

6249

AN:

136260

Hom.:

178

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0725

Gnomad AMI

AF:

0.0189

Gnomad AMR

AF:

0.0264

Gnomad ASJ

AF:

0.0257

Gnomad EAS

AF:

0.0149

Gnomad SAS

AF:

0.0204

Gnomad FIN

AF:

0.0383

Gnomad MID

AF:

0.0174

Gnomad NFE

AF:

0.0414

Gnomad OTH

AF:

0.0344

GnomAD4 exome

AF:

0.141

AC:

45216

AN:

321082

Hom.:

Cov.:

AF XY:

0.140

AC XY:

23978

AN XY:

171750

show subpopulations

Gnomad4 AFR exome

AF:

0.166

Gnomad4 AMR exome

AF:

0.134

Gnomad4 ASJ exome

AF:

0.139

Gnomad4 EAS exome

AF:

0.130

Gnomad4 SAS exome

AF:

0.131

Gnomad4 FIN exome

AF:

0.138

Gnomad4 NFE exome

AF:

0.144

Gnomad4 OTH exome

AF:

0.137

GnomAD4 genome

AF:

0.0459

AC:

6256

AN:

136268

Hom.:

178

Cov.:

AF XY:

0.0445

AC XY:

2928

AN XY:

65756

show subpopulations

Gnomad4 AFR

AF:

0.0726

Gnomad4 AMR

AF:

0.0263

Gnomad4 ASJ

AF:

0.0257

Gnomad4 EAS

AF:

0.0149

Gnomad4 SAS

AF:

0.0196

Gnomad4 FIN

AF:

0.0383

Gnomad4 NFE

AF:

0.0414

Gnomad4 OTH

AF:

0.0369

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

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