chr11-58945502-G-T

Variant names:

• chr11-58945502-G-T
• rs502231
• NM_001389712.2:c.-42-1544G>T

Variant summary

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

The NM_001389712.2(GLYATL1):​c.-42-1544G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0371 in 152,216 control chromosomes in the GnomAD database, including 329 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 0.037 (329 hom., cov: 32)
• Consequence: GLYATL1 NM_001389712.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0550
• Publications: 1 publications found

Genes affected

GLYATL1 (HGNC:30519): (glycine-N-acyltransferase like 1) Enables glutamine N-acyltransferase activity. Involved in glutamine metabolic process. Predicted to be located in mitochondrion. [provided by Alliance of Genome Resources, Apr 2022]

ENSG00000255240 (HGNC:58086):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.12 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001389712.2. 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
	GLYATL1	NM_001389712.2	MANE Select	c.-42-1544G>T		intron	N/A	NP_001376641.1
	GLYATL1	NM_080661.6		c.149-1544G>T		intron	N/A	NP_542392.2
	GLYATL1	NM_001220494.4		c.-42-1544G>T		intron	N/A	NP_001207423.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GLYATL1	ENST00000532726.6	TSL:3 MANE Select	c.-42-1544G>T		intron	N/A	ENSP00000436116.2
	GLYATL1	ENST00000317391.8	TSL:1	c.-42-1544G>T		intron	N/A	ENSP00000322223.4
	GLYATL1	ENST00000527708.5	TSL:1	n.149-1544G>T		intron	N/A	ENSP00000434757.1

Frequencies

GnomAD3 genomes AF: 0.0371 AC: 5641 AN: 152098 Hom.: 329 Cov.: 32

Gnomad AFR AF: 0.123

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0139

Gnomad ASJ AF: 0.00895

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00145

Gnomad FIN AF: 0.000565

Gnomad MID AF: 0.0348

Gnomad NFE AF: 0.00340

Gnomad OTH AF: 0.0335

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

GnomAD4 genome AF: 0.0371 AC: 5654 AN: 152216 Hom.: 329 Cov.: 32 AF XY: 0.0354 AC XY: 2634 AN XY: 74430

African (AFR) AF: 0.123 AC: 5086 AN: 41502

American (AMR) AF: 0.0139 AC: 213 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.00895 AC: 31 AN: 3464

East Asian (EAS) AF: 0.00 AC: 0 AN: 5186

South Asian (SAS) AF: 0.00145 AC: 7 AN: 4826

European-Finnish (FIN) AF: 0.000565 AC: 6 AN: 10612

Middle Eastern (MID) AF: 0.0340 AC: 10 AN: 294

European-Non Finnish (NFE) AF: 0.00340 AC: 231 AN: 68012

Other (OTH) AF: 0.0332 AC: 70 AN: 2110

Alfa AF: 0.0274 Hom.: 29

Bravo AF: 0.0416

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.2
PhyloP100		-0.055

Splicing

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

Other links and lift over

dbSNP: rs502231; hg19: chr11-58712975;