11-58838322-A-G

Variant names:

• chr11-58838322-A-G
• rs201184601
• NM_145016.4:c.125T>C

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2 BP4_Moderate

The NM_145016.4(GLYATL2):​c.125T>C​(p.Met42Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 32)
• Consequence: GLYATL2 NM_145016.4 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.30

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]

ACMG classification

Verdict is Uncertain_significance. Variant got 0 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.2431407).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GLYATL2	NM_145016.4	c.125T>C	p.Met42Thr	missense_variant	Exon 3 of 6	ENST00000287275.6	NP_659453.3
GLYATL2	XM_047426545.1	c.2T>C	p.Met1?	start_lost	Exon 2 of 5		XP_047282501.1
GLYATL2	XM_017017337.3	c.125T>C	p.Met42Thr	missense_variant	Exon 4 of 7		XP_016872826.1
GLYATL2	XM_017017338.3	c.125T>C	p.Met42Thr	missense_variant	Exon 3 of 6		XP_016872827.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GLYATL2	ENST00000287275.6	c.125T>C	p.Met42Thr	missense_variant	Exon 3 of 6	1	NM_145016.4	ENSP00000287275.1
GLYATL2	ENST00000532258.1	c.125T>C	p.Met42Thr	missense_variant	Exon 4 of 7	1		ENSP00000434277.1
GLYATL2	ENST00000533636.1	n.107T>C		non_coding_transcript_exon_variant	Exon 2 of 5	3

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 30

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Uncertain	0.38
BayesDel_addAF	Benign	-0.28	T
BayesDel_noAF	Benign	-0.64
CADD	Benign	17
DANN	Benign	0.97
DEOGEN2	Benign	0.025	T;T
Eigen	Benign	-0.54
Eigen_PC	Benign	-0.52
FATHMM_MKL	Benign	0.14	N
LIST_S2	Benign	0.67	.;T
M_CAP	Benign	0.0051	T
MetaRNN	Benign	0.24	T;T
MetaSVM	Benign	-1.0	T
MutationAssessor	Uncertain	2.0	M;M
PrimateAI	Uncertain	0.56	T
PROVEAN	Uncertain	-3.3	D;D
REVEL	Benign	0.067
Sift	Uncertain	0.014	D;D
Sift4G	Uncertain	0.0020	D;D
Polyphen		0.13	B;B
Vest4		0.37
MutPred		0.74		Gain of loop (P = 0.069);Gain of loop (P = 0.069);
MVP		0.081
MPC		0.026
ClinPred		0.40	T
GERP RS		3.6
Varity_R		0.32
gMVP		0.24

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs201184601; hg19: chr11-58605795;