16-1796475-G-C

Variant names:

• chr16-1796475-G-C
• rs344352
• ENST00000564445.5:c.*46-755C>G

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
HAGH	ENST00000564445.5	c.*46-755C>G		intron_variant	Intron 8 of 8	3		ENSP00000455355.1

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;