Variant 10-17594183-G-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_014241.4(HACD1):c.784+22C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.258 in 1,356,336 control chromosomes in the GnomAD database, including 47,594 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.25 ( 4858 hom., cov: 33)

Exomes 𝑓: 0.26 ( 42736 hom. )

Consequence

HACD1
NM_014241.4 intron

Scores

Clinical Significance

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

Conservation

PhyloP100: 0.253

Variant links:

Genes affected

HACD1 (HGNC:9639): (3-hydroxyacyl-CoA dehydratase 1) The protein encoded by this gene contains a characteristic catalytic motif of the protein tyrosine phosphatases (PTPs) family. The PTP motif of this protein has the highly conserved arginine residue replaced by a proline residue; thus it may represent a distinct class of PTPs. Members of the PTP family are known to be signaling molecules that regulate a variety of cellular processes. This gene was preferentially expressed in both adult and fetal heart. A much lower expression level was detected in skeletal and smooth muscle tissues, and no expression was observed in other tissues. The tissue specific expression in the developing and adult heart suggests a role in regulating cardiac development and differentiation. [provided by RefSeq, Jul 2008]

HACD1 links:

HACD1 (HGNC:):

HACD1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.85).

BP6

Variant 10-17594183-G-C is Benign according to our data. Variant chr10-17594183-G-C is described in ClinVar as [Benign]. Clinvar id is 1259757.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.28 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
HACD1	NM_014241.4 linkuse as main transcript	c.784+22C>G		intron_variant		ENST00000361271.8	NP_055056.3	B0YJ81-1
HACD1	XM_005252641.5 linkuse as main transcript	c.676+22C>G		intron_variant			XP_005252698.1

Ensembl

Gene	Transcript	HGVSc	Effect	TSL	MANE	Protein	UniProt
HACD1	ENST00000361271.8 linkuse as main transcript	c.784+22C>G	intron_variant	1	NM_014241.4	ENSP00000355308.3	B0YJ81-1
HACD1	ENST00000498812.5 linkuse as main transcript	n.*173+22C>G	intron_variant	5		ENSP00000462868.1	J3KT94
HACD1	ENST00000471481.1 linkuse as main transcript	n.*26C>G	downstream_gene_variant	3

Frequencies

GnomAD3 genomes

AF:

0.246

AC:

37311

AN:

151914

Hom.:

4853

Cov.:

show subpopulations

Gnomad AFR

AF:

0.229

Gnomad AMI

AF:

0.324

Gnomad AMR

AF:

0.187

Gnomad ASJ

AF:

0.347

Gnomad EAS

AF:

0.0503

Gnomad SAS

AF:

0.180

Gnomad FIN

AF:

0.237

Gnomad MID

AF:

0.255

Gnomad NFE

AF:

0.283

Gnomad OTH

AF:

0.246

GnomAD3 exomes

AF:

0.220

AC:

34506

AN:

156876

Hom.:

4317

AF XY:

0.222

AC XY:

19058

AN XY:

85706

show subpopulations

Gnomad AFR exome

AF:

0.216

Gnomad AMR exome

AF:

0.106

Gnomad ASJ exome

AF:

0.282

Gnomad EAS exome

AF:

0.0503

Gnomad SAS exome

AF:

0.154

Gnomad FIN exome

AF:

0.240

Gnomad NFE exome

AF:

0.269

Gnomad OTH exome

AF:

0.216

GnomAD4 exome

AF:

0.259

AC:

312132

AN:

1204304

Hom.:

42736

Cov.:

AF XY:

0.259

AC XY:

151369

AN XY:

585108

show subpopulations

Gnomad4 AFR exome

AF:

0.216

Gnomad4 AMR exome

AF:

0.124

Gnomad4 ASJ exome

AF:

0.314

Gnomad4 EAS exome

AF:

0.0328

Gnomad4 SAS exome

AF:

0.156

Gnomad4 FIN exome

AF:

0.236

Gnomad4 NFE exome

AF:

0.277

Gnomad4 OTH exome

AF:

0.246

GnomAD4 genome

AF:

0.246

AC:

37325

AN:

152032

Hom.:

4858

Cov.:

AF XY:

0.239

AC XY:

17777

AN XY:

74314

show subpopulations

Gnomad4 AFR

AF:

0.229

Gnomad4 AMR

AF:

0.186

Gnomad4 ASJ

AF:

0.347

Gnomad4 EAS

AF:

0.0502

Gnomad4 SAS

AF:

0.179

Gnomad4 FIN

AF:

0.237

Gnomad4 NFE

AF:

0.283

Gnomad4 OTH

AF:

0.245

Alfa

AF:

0.246

Hom.:

1000

Bravo

AF:

0.240

Asia WGS

AF:

0.123

AC:

428

AN:

3470

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Jun 19, 2021	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.85

CADD

Benign

1.6

DANN

Benign

0.63

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.040

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