rs2507838

Positions:

• chr11-58705326-C-A
• chr11-58705326-C-G
• chr11-58705326-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000586098.1(GLYAT):​c.90+7434G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0629 in 152,084 control chromosomes in the GnomAD database, including 670 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 0.063 (670 hom., cov: 32)
• Consequence: GLYAT ENST00000586098.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.117

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=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.17 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
GLYAT	ENST00000586098.1	c.90+7434G>T		intron_variant		3		ENSP00000468512

Frequencies

GnomAD3 genomes AF: 0.0629 AC: 9563 AN: 151966 Hom.: 670 Cov.: 32

Gnomad AFR AF: 0.174

Gnomad AMI AF: 0.0175

Gnomad AMR AF: 0.0239

Gnomad ASJ AF: 0.0363

Gnomad EAS AF: 0.0376

Gnomad SAS AF: 0.0496

Gnomad FIN AF: 0.00349

Gnomad MID AF: 0.0190

Gnomad NFE AF: 0.0191

Gnomad OTH AF: 0.0468

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

GnomAD4 genome AF: 0.0629 AC: 9573 AN: 152084 Hom.: 670 Cov.: 32 AF XY: 0.0602 AC XY: 4474 AN XY: 74368

Gnomad4 AFR AF: 0.173

Gnomad4 AMR AF: 0.0239

Gnomad4 ASJ AF: 0.0363

Gnomad4 EAS AF: 0.0373

Gnomad4 SAS AF: 0.0492

Gnomad4 FIN AF: 0.00349

Gnomad4 NFE AF: 0.0191

Gnomad4 OTH AF: 0.0478

Alfa AF: 0.0110 Hom.: 4

Bravo AF: 0.0689

Asia WGS AF: 0.0580 AC: 203 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	2.0
DANN	Benign	0.11

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2507838; hg19: chr11-58472799;