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

Frequency

Genomes: 𝑓 0.037 ( 168 hom., cov: 0)

Exomes 𝑓: 0.032 ( 64 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-ATTT is Benign according to our data. Variant chr2-190208668-A-ATTT is described in ClinVar as [Benign]. Clinvar id is 1221023.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.15 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+212insAAA		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+212insAAA		intron_variant		1	NM_014362.4	P1	Q6NVY1-1

Frequencies

GnomAD3 genomes

AF:

0.0367

AC:

5004

AN:

136272

Hom.:

164

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0519

Gnomad AMI

AF:

0.00946

Gnomad AMR

AF:

0.0196

Gnomad ASJ

AF:

0.0166

Gnomad EAS

AF:

0.159

Gnomad SAS

AF:

0.0704

Gnomad FIN

AF:

0.0126

Gnomad MID

AF:

0.0278

Gnomad NFE

AF:

0.0245

Gnomad OTH

AF:

0.0355

GnomAD4 exome

AF:

0.0316

AC:

10274

AN:

325208

Hom.:

Cov.:

AF XY:

0.0323

AC XY:

5615

AN XY:

174046

show subpopulations

Gnomad4 AFR exome

AF:

0.0509

Gnomad4 AMR exome

AF:

0.0210

Gnomad4 ASJ exome

AF:

0.0181

Gnomad4 EAS exome

AF:

0.105

Gnomad4 SAS exome

AF:

0.0486

Gnomad4 FIN exome

AF:

0.0135

Gnomad4 NFE exome

AF:

0.0241

Gnomad4 OTH exome

AF:

0.0297

GnomAD4 genome

AF:

0.0368

AC:

5010

AN:

136280

Hom.:

168

Cov.:

AF XY:

0.0374

AC XY:

2457

AN XY:

65760

show subpopulations

Gnomad4 AFR

AF:

0.0521

Gnomad4 AMR

AF:

0.0195

Gnomad4 ASJ

AF:

0.0166

Gnomad4 EAS

AF:

0.160

Gnomad4 SAS

AF:

0.0698

Gnomad4 FIN

AF:

0.0126

Gnomad4 NFE

AF:

0.0245

Gnomad4 OTH

AF:

0.0353

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 21, 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