chr16-1795604-C-T

Variant names:

• chr16-1795604-C-T
• rs3764349
• ENST00000564445.5:c.*162G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.03
• Publications: 1 publications found

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

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	c.*162G>A		downstream_gene_variant		3		ENSP00000455355.1

Frequencies

GnomAD3 genomes AF: 0.191 AC: 29070 AN: 151978 Hom.: 4385 Cov.: 32

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: 8 AN: 112 Hom.: 0 Cov.: 0 AF XY: 0.0541 AC XY: 4 AN XY: 74

African (AFR) AC: 0 AN: 0

American (AMR) AF: 0.125 AC: 1 AN: 8

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 2

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AF: 0.00 AC: 0 AN: 4

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 6

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.0581 AC: 5 AN: 86

Other (OTH) AF: 0.333 AC: 2 AN: 6

GnomAD4 genome AF: 0.191 AC: 29118 AN: 152096 Hom.: 4399 Cov.: 32 AF XY: 0.188 AC XY: 14007 AN XY: 74376

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: 27 AN: 294

European-Non Finnish (NFE) AF: 0.0992 AC: 6744 AN: 67976

Other (OTH) AF: 0.176 AC: 372 AN: 2110

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
DANN	Benign	0.32
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs3764349; hg19: chr16-1845605;