Variant 10-17594086-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1

The NM_014241.4(HACD1):c.784+119C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.246 in 947,910 control chromosomes in the GnomAD database, including 30,319 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.25 ( 5036 hom., cov: 32)

Exomes 𝑓: 0.25 ( 25283 hom. )

Consequence

HACD1
NM_014241.4 intron

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.410

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:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.89).

BP6

Variant 10-17594086-G-A is Benign according to our data. Variant chr10-17594086-G-A is described in ClinVar as [Benign]. Clinvar id is 1264544.Status of the report is criteria_provided_single_submitter, 1 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 link	c.784+119C>T		intron_variant		ENST00000361271.8	NP_055056.3	B0YJ81-1
HACD1	XM_005252641.5 link	c.676+119C>T		intron_variant			XP_005252698.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
HACD1	ENST00000361271.8 link	c.784+119C>T		intron_variant		1	NM_014241.4	ENSP00000355308.3		B0YJ81-1
HACD1	ENST00000498812.5 link	n.*173+119C>T		intron_variant		5		ENSP00000462868.1		J3KT94

Frequencies

GnomAD3 genomes

AF:

0.250

AC:

38011

AN:

151858

Hom.:

5031

Cov.:

show subpopulations

Gnomad AFR

AF:

0.246

Gnomad AMI

AF:

0.326

Gnomad AMR

AF:

0.190

Gnomad ASJ

AF:

0.346

Gnomad EAS

AF:

0.0511

Gnomad SAS

AF:

0.168

Gnomad FIN

AF:

0.238

Gnomad MID

AF:

0.259

Gnomad NFE

AF:

0.283

Gnomad OTH

AF:

0.248

GnomAD4 exome

AF:

0.246

AC:

195618

AN:

795938

Hom.:

25283

AF XY:

0.246

AC XY:

94668

AN XY:

384616

show subpopulations

Gnomad4 AFR exome

AF:

0.223

Gnomad4 AMR exome

AF:

0.138

Gnomad4 ASJ exome

AF:

0.315

Gnomad4 EAS exome

AF:

0.0292

Gnomad4 SAS exome

AF:

0.142

Gnomad4 FIN exome

AF:

0.232

Gnomad4 NFE exome

AF:

0.260

Gnomad4 OTH exome

AF:

0.237

GnomAD4 genome

AF:

0.250

AC:

38028

AN:

151972

Hom.:

5036

Cov.:

AF XY:

0.243

AC XY:

18088

AN XY:

74284

show subpopulations

Gnomad4 AFR

AF:

0.246

Gnomad4 AMR

AF:

0.189

Gnomad4 ASJ

AF:

0.346

Gnomad4 EAS

AF:

0.0510

Gnomad4 SAS

AF:

0.167

Gnomad4 FIN

AF:

0.238

Gnomad4 NFE

AF:

0.283

Gnomad4 OTH

AF:

0.247

Alfa

AF:

0.176

Hom.:

456

Bravo

AF:

0.247

Asia WGS

AF:

0.120

AC:

416

AN:

3468

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

Jun 19, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.89

CADD

Benign

2.6

DANN

Benign

0.62

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