rs187660800

Variant names:

• chr11-58834799-T-C
• rs187660800
• NM_145016.4:c.515A>G

Your query was ambiguous. Multiple possible variants found:

• chr11-58834799-T-C
• chr11-58834799-T-G

Variant summary

Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2 PP3

The NM_145016.4(GLYATL2):​c.515A>G​(p.His172Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000137 in 1,457,690 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: not found (cov: 32)
  • Exomes 𝑓: 0.0000014 (0 hom.)
• Consequence: GLYATL2 NM_145016.4 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.42

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 3 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• PP3: MetaRNN computational evidence supports a deleterious effect, 0.796

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GLYATL2	NM_145016.4	c.515A>G	p.His172Arg	missense_variant	Exon 6 of 6	ENST00000287275.6	NP_659453.3
GLYATL2	XM_017017337.3	c.515A>G	p.His172Arg	missense_variant	Exon 7 of 7		XP_016872826.1
GLYATL2	XM_017017338.3	c.515A>G	p.His172Arg	missense_variant	Exon 6 of 6		XP_016872827.1
GLYATL2	XM_047426545.1	c.392A>G	p.His131Arg	missense_variant	Exon 5 of 5		XP_047282501.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GLYATL2	ENST00000287275.6	c.515A>G	p.His172Arg	missense_variant	Exon 6 of 6	1	NM_145016.4	ENSP00000287275.1
GLYATL2	ENST00000532258.1	c.515A>G	p.His172Arg	missense_variant	Exon 7 of 7	1		ENSP00000434277.1
GLYATL2	ENST00000533636.1	n.497A>G		non_coding_transcript_exon_variant	Exon 5 of 5	3

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome AF: 0.00000137 AC: 2 AN: 1457690 Hom.: 0 Cov.: 31 AF XY: 0.00000138 AC XY: 1 AN XY: 724936

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 9.00e-7

Gnomad4 OTH exome AF: 0.0000166

GnomAD4 genome Cov.: 32

Bravo AF: 0.00000378

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.22
BayesDel_addAF	Benign	-0.11	T
BayesDel_noAF	Benign	-0.39
CADD	Benign	19
DANN	Benign	0.92
DEOGEN2	Benign	0.21	T;T
Eigen	Benign	0.049
Eigen_PC	Benign	-0.15
FATHMM_MKL	Benign	0.17	N
LIST_S2	Benign	0.61	.;T
M_CAP	Benign	0.0038	T
MetaRNN	Pathogenic	0.80	D;D
MetaSVM	Benign	-1.0	T
MutationAssessor	Pathogenic	3.0	M;M
PrimateAI	Uncertain	0.60	T
PROVEAN	Pathogenic	-6.9	D;D
REVEL	Benign	0.17
Sift	Uncertain	0.0030	D;D
Sift4G	Uncertain	0.0090	D;D
Polyphen		0.98	D;D
Vest4		0.40
MutPred		0.86		Gain of relative solvent accessibility (P = 0.1259);Gain of relative solvent accessibility (P = 0.1259);
MVP		0.34
MPC		0.12
ClinPred		0.94	D
GERP RS		4.2
Varity_R		0.60
gMVP		0.64

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: rs187660800; hg19: chr11-58602272; COSMIC: COSV99780513;