chr11-58834800-G-T

Variant names:

• chr11-58834800-G-T
• rs747413442
• NM_145016.4:c.514C>A

Variant summary

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

The NM_145016.4(GLYATL2):​c.514C>A​(p.His172Asn) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000686 in 1,457,244 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. H172P) has been classified as Uncertain significance.

• Frequency:
  • Genomes: not found (cov: 32)
  • Exomes 𝑓: 6.9e-7 (0 hom.)
• Consequence: GLYATL2 NM_145016.4 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.480

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 2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GLYATL2	NM_145016.4	c.514C>A	p.His172Asn	missense_variant	Exon 6 of 6	ENST00000287275.6	NP_659453.3
GLYATL2	XM_017017337.3	c.514C>A	p.His172Asn	missense_variant	Exon 7 of 7		XP_016872826.1
GLYATL2	XM_017017338.3	c.514C>A	p.His172Asn	missense_variant	Exon 6 of 6		XP_016872827.1
GLYATL2	XM_047426545.1	c.391C>A	p.His131Asn	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.514C>A	p.His172Asn	missense_variant	Exon 6 of 6	1	NM_145016.4	ENSP00000287275.1
GLYATL2	ENST00000532258.1	c.514C>A	p.His172Asn	missense_variant	Exon 7 of 7	1		ENSP00000434277.1
GLYATL2	ENST00000533636.1	n.496C>A		non_coding_transcript_exon_variant	Exon 5 of 5	3

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD3 exomes AF: 0.00000822 AC: 2 AN: 243242 Hom.: 0 AF XY: 0.0000152 AC XY: 2 AN XY: 131922

Gnomad AFR exome AF: 0.00

Gnomad AMR exome AF: 0.00

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.00

Gnomad SAS exome AF: 0.00

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.0000180

Gnomad OTH exome AF: 0.00

GnomAD4 exome AF: 6.86e-7 AC: 1 AN: 1457244 Hom.: 0 Cov.: 31 AF XY: 0.00000138 AC XY: 1 AN XY: 724700

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: 0.00

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.14
BayesDel_addAF	Benign	-0.27	T
BayesDel_noAF	Benign	-0.60
CADD	Benign	14
DANN	Benign	0.77
DEOGEN2	Benign	0.072	T;T
Eigen	Benign	-0.42
Eigen_PC	Benign	-0.63
FATHMM_MKL	Benign	0.050	N
LIST_S2	Benign	0.61	.;T
M_CAP	Benign	0.0021	T
MetaRNN	Uncertain	0.66	D;D
MetaSVM	Benign	-1.1	T
MutationAssessor	Uncertain	2.3	M;M
PrimateAI	Uncertain	0.60	T
PROVEAN	Pathogenic	-5.9	D;D
REVEL	Benign	0.091
Sift	Benign	0.090	T;T
Sift4G	Benign	0.18	T;T
Polyphen		0.99	D;D
Vest4		0.25
MutPred		0.86		Loss of helix (P = 0.1299);Loss of helix (P = 0.1299);
MVP		0.37
MPC		0.11
ClinPred		0.79	D
GERP RS		0.99
Varity_R		0.20
gMVP		0.52

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: rs747413442; hg19: chr11-58602273;