11-58901210-C-T

Variant names:

• chr11-58901210-C-T
• rs2187267
• XM_017017338.3:c.-41+3817G>A

Variant summary

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

The ENST00000533636.1(GLYATL2):​n.60+2946G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.938 in 152,232 control chromosomes in the GnomAD database, including 67,655 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 0.94 (67655 hom., cov: 31)
• Consequence: GLYATL2 ENST00000533636.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.73
• Publications: 1 publications found

Genes affected

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]

ENSG00000299851 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.99 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000533636.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

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

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GLYATL2	ENST00000533636.1	TSL:3	n.60+2946G>A		intron	N/A
	ENSG00000299851	ENST00000766842.1		n.823-1452G>A		intron	N/A
	ENSG00000299851	ENST00000766843.1		n.823+3817G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.938 AC: 142715 AN: 152114 Hom.: 67616 Cov.: 31

Gnomad AFR AF: 0.792

Gnomad AMI AF: 1.00

Gnomad AMR AF: 0.977

Gnomad ASJ AF: 0.990

Gnomad EAS AF: 1.00

Gnomad SAS AF: 0.998

Gnomad FIN AF: 0.999

Gnomad MID AF: 0.968

Gnomad NFE AF: 0.996

Gnomad OTH AF: 0.947

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

GnomAD4 genome AF: 0.938 AC: 142813 AN: 152232 Hom.: 67655 Cov.: 31 AF XY: 0.941 AC XY: 70038 AN XY: 74440

African (AFR) AF: 0.792 AC: 32865 AN: 41492

American (AMR) AF: 0.977 AC: 14959 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.990 AC: 3437 AN: 3472

East Asian (EAS) AF: 1.00 AC: 5160 AN: 5160

South Asian (SAS) AF: 0.998 AC: 4812 AN: 4822

European-Finnish (FIN) AF: 0.999 AC: 10617 AN: 10624

Middle Eastern (MID) AF: 0.969 AC: 285 AN: 294

European-Non Finnish (NFE) AF: 0.996 AC: 67760 AN: 68036

Other (OTH) AF: 0.948 AC: 2006 AN: 2116

Alfa AF: 0.960 Hom.: 9528

Bravo AF: 0.929

Asia WGS AF: 0.986 AC: 3430 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	0.69
DANN	Benign	0.38
PhyloP100		-1.7

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs2187267;

hg19: chr11-58668683;