chr11-58654390-G-C

Variant names:

• chr11-58654390-G-C
• rs1009172
• ENST00000586098.1:c.89-11135C>G

Variant summary

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

The ENST00000586098.1(GLYAT):​c.89-11135C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.407 in 151,968 control chromosomes in the GnomAD database, including 12,723 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 0.41 (12723 hom., cov: 32)
• Consequence: GLYAT ENST00000586098.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.833
• Publications: 2 publications found

Genes affected

GLYAT (HGNC:13734): (glycine-N-acyltransferase) The glycine-N-acyltransferase protein conjugates glycine with acyl-CoA substrates in the mitochondria. The protein is thought to be important in the detoxification of endogenous and xenobiotic acyl-CoA's. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.434 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000586098.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GLYAT	ENST00000586098.1	TSL:3	c.89-11135C>G		intron	N/A	ENSP00000468512.1

Frequencies

GnomAD3 genomes AF: 0.407 AC: 61743 AN: 151848 Hom.: 12709 Cov.: 32

Gnomad AFR AF: 0.386

Gnomad AMI AF: 0.423

Gnomad AMR AF: 0.399

Gnomad ASJ AF: 0.392

Gnomad EAS AF: 0.318

Gnomad SAS AF: 0.450

Gnomad FIN AF: 0.500

Gnomad MID AF: 0.545

Gnomad NFE AF: 0.410

Gnomad OTH AF: 0.408

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

GnomAD4 genome AF: 0.407 AC: 61793 AN: 151968 Hom.: 12723 Cov.: 32 AF XY: 0.410 AC XY: 30481 AN XY: 74270

African (AFR) AF: 0.386 AC: 16008 AN: 41456

American (AMR) AF: 0.399 AC: 6087 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.392 AC: 1360 AN: 3470

East Asian (EAS) AF: 0.317 AC: 1637 AN: 5156

South Asian (SAS) AF: 0.450 AC: 2166 AN: 4818

European-Finnish (FIN) AF: 0.500 AC: 5273 AN: 10554

Middle Eastern (MID) AF: 0.558 AC: 163 AN: 292

European-Non Finnish (NFE) AF: 0.410 AC: 27857 AN: 67942

Other (OTH) AF: 0.406 AC: 856 AN: 2106

Alfa AF: 0.413 Hom.: 1652

Bravo AF: 0.396

Asia WGS AF: 0.376 AC: 1306 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	5.4
DANN	Benign	0.58
PhyloP100		0.83

Splicing

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

Other links and lift over

dbSNP: rs1009172; hg19: chr11-58421863;