16-1796475-G-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000564445.5(HAGH):c.*46-755C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.702 in 152,016 control chromosomes in the GnomAD database, including 37,602 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 0.70 (37602 hom., cov: 32)
• Consequence: HAGH ENST00000564445.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00400

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.734 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
HAGH	ENST00000564445.5	c.*46-755C>G		intron_variant		3

Frequencies

GnomAD3 genomes AF: 0.702 AC: 106568 AN: 151900 Hom.: 37561 Cov.: 32

Gnomad AFR AF: 0.741

Gnomad AMI AF: 0.820

Gnomad AMR AF: 0.698

Gnomad ASJ AF: 0.742

Gnomad EAS AF: 0.598

Gnomad SAS AF: 0.673

Gnomad FIN AF: 0.576

Gnomad MID AF: 0.788

Gnomad NFE AF: 0.704

Gnomad OTH AF: 0.712

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.702 AC: 106662 AN: 152016 Hom.: 37602 Cov.: 32 AF XY: 0.694 AC XY: 51550 AN XY: 74322

Gnomad4 AFR AF: 0.740

Gnomad4 AMR AF: 0.698

Gnomad4 ASJ AF: 0.742

Gnomad4 EAS AF: 0.599

Gnomad4 SAS AF: 0.672

Gnomad4 FIN AF: 0.576

Gnomad4 NFE AF: 0.704

Gnomad4 OTH AF: 0.716

Alfa AF: 0.596 Hom.: 1625

Bravo AF: 0.717

Asia WGS AF: 0.642 AC: 2233 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	1.4
Dann	Benign	0.42

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs344352; hg19: chr16-1846476;