rs1456114

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_198402.5(HACD2):​c.381+2081C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.545 in 152,096 control chromosomes in the GnomAD database, including 25,327 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.55 ( 25327 hom., cov: 32)

Consequence

HACD2
NM_198402.5 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.88
Variant links:
Genes affected
HACD2 (HGNC:9640): (3-hydroxyacyl-CoA dehydratase 2) The protein encoded by this gene can catalyze the third step (dehydration) in the conversion of long chain fatty acids to very long chain fatty acids. The encoded protein localizes to the endoplasmic reticulum membrane. [provided by RefSeq, Jul 2016]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.9).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.681 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
HACD2NM_198402.5 linkuse as main transcriptc.381+2081C>T intron_variant ENST00000383657.10

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
HACD2ENST00000383657.10 linkuse as main transcriptc.381+2081C>T intron_variant 1 NM_198402.5 P1
HACD2ENST00000469317.1 linkuse as main transcriptc.48+2081C>T intron_variant 3

Frequencies

GnomAD3 genomes
AF:
0.545
AC:
82892
AN:
151978
Hom.:
25332
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.267
Gnomad AMI
AF:
0.618
Gnomad AMR
AF:
0.530
Gnomad ASJ
AF:
0.655
Gnomad EAS
AF:
0.357
Gnomad SAS
AF:
0.609
Gnomad FIN
AF:
0.764
Gnomad MID
AF:
0.599
Gnomad NFE
AF:
0.686
Gnomad OTH
AF:
0.575
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.545
AC:
82918
AN:
152096
Hom.:
25327
Cov.:
32
AF XY:
0.548
AC XY:
40745
AN XY:
74362
show subpopulations
Gnomad4 AFR
AF:
0.268
Gnomad4 AMR
AF:
0.530
Gnomad4 ASJ
AF:
0.655
Gnomad4 EAS
AF:
0.356
Gnomad4 SAS
AF:
0.608
Gnomad4 FIN
AF:
0.764
Gnomad4 NFE
AF:
0.686
Gnomad4 OTH
AF:
0.574
Alfa
AF:
0.606
Hom.:
5052
Bravo
AF:
0.512
Asia WGS
AF:
0.484
AC:
1680
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.90
CADD
Benign
0.064
DANN
Benign
0.82

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.

Other links and lift over

dbSNP: rs1456114; hg19: chr3-123245152; API