11-58914676-T-C

Variant names:

• chr11-58914676-T-C
• rs1892866
• NM_001354699.4:c.-167+7121T>C

Variant summary

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

The NM_001354699.4(GLYATL1):​c.-167+7121T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.459 in 151,998 control chromosomes in the GnomAD database, including 16,992 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 0.46 (16992 hom., cov: 31)
• Consequence: GLYATL1 NM_001354699.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.294
• Publications: 0 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]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.542 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001354699.4. 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
	GLYATL1	NM_001354699.4		c.-167+7121T>C		intron	N/A	NP_001341628.1	Q969I3-1
	GLYATL1	NM_001389714.2		c.-167+9015T>C		intron	N/A	NP_001376643.1	Q969I3-1
	GLYATL1	NM_001389717.2		c.-212+7121T>C		intron	N/A	NP_001376646.1	Q969I3-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GLYATL1	ENST00000534674.5	TSL:4	n.264+9015T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.459 AC: 69700 AN: 151880 Hom.: 16994 Cov.: 31

Gnomad AFR AF: 0.282

Gnomad AMI AF: 0.615

Gnomad AMR AF: 0.508

Gnomad ASJ AF: 0.416

Gnomad EAS AF: 0.419

Gnomad SAS AF: 0.462

Gnomad FIN AF: 0.525

Gnomad MID AF: 0.453

Gnomad NFE AF: 0.547

Gnomad OTH AF: 0.489

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

GnomAD4 genome AF: 0.459 AC: 69712 AN: 151998 Hom.: 16992 Cov.: 31 AF XY: 0.458 AC XY: 34030 AN XY: 74278

African (AFR) AF: 0.282 AC: 11669 AN: 41444

American (AMR) AF: 0.508 AC: 7765 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.416 AC: 1444 AN: 3468

East Asian (EAS) AF: 0.419 AC: 2166 AN: 5166

South Asian (SAS) AF: 0.463 AC: 2234 AN: 4822

European-Finnish (FIN) AF: 0.525 AC: 5539 AN: 10552

Middle Eastern (MID) AF: 0.463 AC: 136 AN: 294

European-Non Finnish (NFE) AF: 0.547 AC: 37176 AN: 67950

Other (OTH) AF: 0.485 AC: 1022 AN: 2108

Alfa AF: 0.512 Hom.: 10387

Bravo AF: 0.450

Asia WGS AF: 0.449 AC: 1565 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	3.1
DANN	Benign	0.37
PhyloP100		0.29

Splicing

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

Other links and lift over

dbSNP: rs1892866; hg19: chr11-58682149;