rs1009172

Variant names:

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

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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.

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
GLYAT	ENST00000586098.1	c.89-11135C>G		intron_variant	Intron 1 of 2	3		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

Gnomad4 AFR AF: 0.386

Gnomad4 AMR AF: 0.399

Gnomad4 ASJ AF: 0.392

Gnomad4 EAS AF: 0.317

Gnomad4 SAS AF: 0.450

Gnomad4 FIN AF: 0.500

Gnomad4 NFE AF: 0.410

Gnomad4 OTH AF: 0.406

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 v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1009172; hg19: chr11-58421863;