11-58863970-A-G

Variant names:

• chr11-58863970-A-G
• rs496601
• ENST00000529451.2:n.424-14288A>G

Variant summary

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

The ENST00000529451.2(ENSG00000289621):​n.424-14288A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.887 in 152,212 control chromosomes in the GnomAD database, including 61,057 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 0.89 (61057 hom., cov: 33)
• Consequence: ENSG00000289621 ENST00000529451.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.10
• Publications: 1 publications found

Genes affected

ENSG00000289621 (HGNC:):

GLYATL2 (HGNC:24178): (glycine-N-acyltransferase like 2) Enables glycine N-acyltransferase activity. Involved in long-chain fatty acid catabolic process; medium-chain fatty acid catabolic process; and monounsaturated fatty acid catabolic process. Located in endoplasmic reticulum. [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=-1.05).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.972 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000529451.2. 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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000289621	ENST00000529451.2	TSL:2	n.424-14288A>G		intron	N/A
	GLYATL2	ENST00000533636.1	TSL:3	n.61-25602T>C		intron	N/A
	ENSG00000289621	ENST00000766632.1		n.422-20936A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.887 AC: 134968 AN: 152094 Hom.: 61038 Cov.: 33

Gnomad AFR AF: 0.696

Gnomad AMI AF: 0.999

Gnomad AMR AF: 0.920

Gnomad ASJ AF: 0.968

Gnomad EAS AF: 0.847

Gnomad SAS AF: 0.892

Gnomad FIN AF: 0.976

Gnomad MID AF: 0.946

Gnomad NFE AF: 0.979

Gnomad OTH AF: 0.907

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

GnomAD4 genome AF: 0.887 AC: 135036 AN: 152212 Hom.: 61057 Cov.: 33 AF XY: 0.887 AC XY: 66000 AN XY: 74444

African (AFR) AF: 0.696 AC: 28866 AN: 41474

American (AMR) AF: 0.920 AC: 14075 AN: 15306

Ashkenazi Jewish (ASJ) AF: 0.968 AC: 3358 AN: 3470

East Asian (EAS) AF: 0.847 AC: 4377 AN: 5166

South Asian (SAS) AF: 0.893 AC: 4314 AN: 4832

European-Finnish (FIN) AF: 0.976 AC: 10368 AN: 10626

Middle Eastern (MID) AF: 0.949 AC: 279 AN: 294

European-Non Finnish (NFE) AF: 0.979 AC: 66566 AN: 68016

Other (OTH) AF: 0.908 AC: 1922 AN: 2116

Alfa AF: 0.923 Hom.: 8013

Bravo AF: 0.876

Asia WGS AF: 0.872 AC: 3032 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	1.8
DANN	Benign	0.24
PhyloP100		-2.1

Splicing

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

Other links and lift over

dbSNP: rs496601; hg19: chr11-58631443;