rs2507838

Variant names:

• chr11-58705326-C-A
• rs2507838
• ENST00000586098.1:c.88+7434G>T

Your query was ambiguous. Multiple possible variants found:

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

Variant summary

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

The ENST00000586098.1(GLYAT):​c.88+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
• Publications: 10 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=-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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GLYAT	ENST00000586098.1	c.88+7434G>T		intron_variant	Intron 1 of 2	3		ENSP00000468512.1

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

African (AFR) AF: 0.173 AC: 7193 AN: 41464

American (AMR) AF: 0.0239 AC: 365 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.0363 AC: 126 AN: 3472

East Asian (EAS) AF: 0.0373 AC: 193 AN: 5170

South Asian (SAS) AF: 0.0492 AC: 237 AN: 4814

European-Finnish (FIN) AF: 0.00349 AC: 37 AN: 10592

Middle Eastern (MID) AF: 0.0204 AC: 6 AN: 294

European-Non Finnish (NFE) AF: 0.0191 AC: 1299 AN: 67972

Other (OTH) AF: 0.0478 AC: 101 AN: 2114

Alfa AF: 0.0370 Hom.: 460

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
PhyloP100		0.12

Splicing

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

Other links and lift over

dbSNP: rs2507838; hg19: chr11-58472799;