Genetic Variant HAGH:c.*162G>A (chr16-1795604-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000564445.5(HAGH):c.*162G>A variant causes a downstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.191 in 152,208 control chromosomes in the GnomAD database, including 4,399 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 0.19 ( 4399 hom., cov: 32)

Exomes 𝑓: 0.071 ( 0 hom. )

Consequence

HAGH
ENST00000564445.5 downstream_gene

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.03

Publications

1 publications found

Variant links:

Genes affected

HAGH (HGNC:4805): (hydroxyacylglutathione hydrolase) The enzyme encoded by this gene is classified as a thiolesterase and is responsible for the hydrolysis of S-lactoyl-glutathione to reduced glutathione and D-lactate. Three transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Oct 2013]

HAGH links:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.95).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.413 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
HAGH	ENST00000564445.5 link	c.*162G>A		downstream_gene_variant		3		ENSP00000455355.1		H3BPK3

Frequencies

GnomAD3 genomes

AF:

0.191

AC:

29070

AN:

151978

Hom.:

4385

Cov.:

show subpopulations

Gnomad AFR

AF:

0.419

Gnomad AMI

AF:

0.0637

Gnomad AMR

AF:

0.105

Gnomad ASJ

AF:

0.0789

Gnomad EAS

AF:

0.159

Gnomad SAS

AF:

0.248

Gnomad FIN

AF:

0.0661

Gnomad MID

AF:

0.0854

Gnomad NFE

AF:

0.0992

Gnomad OTH

AF:

0.169

GnomAD4 exome

AF:

0.0714

AC:

AN:

112

Hom.:

Cov.:

AF XY:

0.0541

AC XY:

AN XY:

show subpopulations

African (AFR)

AC:

AN:

American (AMR)

AF:

0.125

AC:

AN:

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AF:

0.00

AC:

AN:

European-Finnish (FIN)

AF:

0.00

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.0581

AC:

AN:

Other (OTH)

AF:

0.333

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.444

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.191

AC:

29118

AN:

152096

Hom.:

4399

Cov.:

AF XY:

0.188

AC XY:

14007

AN XY:

74376

show subpopulations

African (AFR)

AF:

0.418

AC:

17339

AN:

41448

American (AMR)

AF:

0.104

AC:

1594

AN:

15280

Ashkenazi Jewish (ASJ)

AF:

0.0789

AC:

274

AN:

3472

East Asian (EAS)

AF:

0.159

AC:

822

AN:

5174

South Asian (SAS)

AF:

0.246

AC:

1187

AN:

4828

European-Finnish (FIN)

AF:

0.0661

AC:

701

AN:

10604

Middle Eastern (MID)

AF:

0.0918

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0992

AC:

6744

AN:

67976

Other (OTH)

AF:

0.176

AC:

372

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1054

2109

3163

4218

5272

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

300

600

900

1200

1500

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.162

Hom.:

365

Bravo

AF:

0.200

Asia WGS

AF:

0.232

AC:

806

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.95

CADD

Benign

5.8

(source)

DANN

Benign

0.32

PhyloP100

-1.0

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over