11-58914676-T-C

Position:

• chr11-58914676-T-C

Variant summary

Our verdict is Benign. Variant got -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

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]

GLYATL1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
GLYATL1	NM_001354699.4	c.-167+7121T>C		intron_variant			NP_001341628.1
GLYATL1	NM_001389714.2	c.-167+9015T>C		intron_variant			NP_001376643.1
GLYATL1	NM_001389717.2	c.-212+7121T>C		intron_variant			NP_001376646.1
GLYATL1	NM_001389718.2	c.-170+9015T>C		intron_variant			NP_001376647.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
GLYATL1	ENST00000534674.5	n.264+9015T>C		intron_variant		4

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

Gnomad4 AFR AF: 0.282

Gnomad4 AMR AF: 0.508

Gnomad4 ASJ AF: 0.416

Gnomad4 EAS AF: 0.419

Gnomad4 SAS AF: 0.463

Gnomad4 FIN AF: 0.525

Gnomad4 NFE AF: 0.547

Gnomad4 OTH AF: 0.485

Alfa AF: 0.513 Hom.: 9278

Bravo AF: 0.450

Asia WGS AF: 0.449 AC: 1565 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1892866; hg19: chr11-58682149;