rs2750007

Variant names:

• chr17-773986-C-T
• rs2750007
• NM_016080.4:c.406+1789G>A

Variant summary

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

The NM_016080.4(GLOD4):​c.406+1789G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0761 in 152,206 control chromosomes in the GnomAD database, including 734 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 0.076 (734 hom., cov: 32)
• Consequence: GLOD4 NM_016080.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.19
• Publications: 5 publications found

Genes affected

GLOD4 (HGNC:14111): (glyoxalase domain containing 4) Enables cadherin binding activity. Located in extracellular exosome. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.325 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_016080.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GLOD4	NM_016080.4	MANE Select	c.406+1789G>A		intron	N/A	NP_057164.3
	GLOD4	NM_001389725.1		c.604+1789G>A		intron	N/A	NP_001376654.1
	GLOD4	NM_001389726.1		c.517+1789G>A		intron	N/A	NP_001376655.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GLOD4	ENST00000301329.11	TSL:1 MANE Select	c.406+1789G>A		intron	N/A	ENSP00000301329.6	Q9HC38-2
	GLOD4	ENST00000301328.9	TSL:1	c.451+1789G>A		intron	N/A	ENSP00000301328.5	Q9HC38-1
	GLOD4	ENST00000891260.1		c.517+1789G>A		intron	N/A	ENSP00000561319.1

Frequencies

GnomAD3 genomes AF: 0.0761 AC: 11574 AN: 152088 Hom.: 734 Cov.: 32

Gnomad AFR AF: 0.0216

Gnomad AMI AF: 0.0450

Gnomad AMR AF: 0.135

Gnomad ASJ AF: 0.0346

Gnomad EAS AF: 0.338

Gnomad SAS AF: 0.121

Gnomad FIN AF: 0.0647

Gnomad MID AF: 0.0605

Gnomad NFE AF: 0.0775

Gnomad OTH AF: 0.0750

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

GnomAD4 genome AF: 0.0761 AC: 11579 AN: 152206 Hom.: 734 Cov.: 32 AF XY: 0.0787 AC XY: 5856 AN XY: 74420

African (AFR) AF: 0.0215 AC: 894 AN: 41554

American (AMR) AF: 0.136 AC: 2072 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.0346 AC: 120 AN: 3472

East Asian (EAS) AF: 0.338 AC: 1742 AN: 5156

South Asian (SAS) AF: 0.121 AC: 582 AN: 4822

European-Finnish (FIN) AF: 0.0647 AC: 686 AN: 10608

Middle Eastern (MID) AF: 0.0582 AC: 17 AN: 292

European-Non Finnish (NFE) AF: 0.0775 AC: 5267 AN: 67996

Other (OTH) AF: 0.0747 AC: 158 AN: 2114

Alfa AF: 0.0773 Hom.: 1268

Bravo AF: 0.0794

Asia WGS AF: 0.203 AC: 703 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	0.79
DANN	Benign	0.63
PhyloP100		-1.2
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs2750007; hg19: chr17-677226;