6-49520574-T-A

Position:

• chr6-49520574-T-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001010904.2(GLYATL3):​c.314-1071T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.465 in 151,988 control chromosomes in the GnomAD database, including 17,304 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 0.47 (17304 hom., cov: 33)
• Consequence: GLYATL3 NM_001010904.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.34

Genes affected

GLYATL3 (HGNC:21349): (glycine-N-acyltransferase like 3) Predicted to enable glycine N-acyltransferase activity. Predicted to be located in mitochondrion. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.6 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
GLYATL3	NM_001010904.2	c.314-1071T>A		intron_variant		ENST00000371197.9	NP_001010904.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
GLYATL3	ENST00000371197.9	c.314-1071T>A		intron_variant		2	NM_001010904.2	ENSP00000360240	P1
GLYATL3	ENST00000545705.1	c.314-1071T>A		intron_variant		5		ENSP00000440029

Frequencies

GnomAD3 genomes AF: 0.465 AC: 70677 AN: 151872 Hom.: 17284 Cov.: 33

Gnomad AFR AF: 0.555

Gnomad AMI AF: 0.477

Gnomad AMR AF: 0.578

Gnomad ASJ AF: 0.376

Gnomad EAS AF: 0.618

Gnomad SAS AF: 0.476

Gnomad FIN AF: 0.480

Gnomad MID AF: 0.462

Gnomad NFE AF: 0.376

Gnomad OTH AF: 0.440

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

GnomAD4 genome AF: 0.465 AC: 70742 AN: 151988 Hom.: 17304 Cov.: 33 AF XY: 0.475 AC XY: 35313 AN XY: 74272

Gnomad4 AFR AF: 0.555

Gnomad4 AMR AF: 0.579

Gnomad4 ASJ AF: 0.376

Gnomad4 EAS AF: 0.618

Gnomad4 SAS AF: 0.474

Gnomad4 FIN AF: 0.480

Gnomad4 NFE AF: 0.376

Gnomad4 OTH AF: 0.444

Alfa AF: 0.437 Hom.: 1867

Bravo AF: 0.479

Asia WGS AF: 0.559 AC: 1942 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.36
DANN	Benign	0.50

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: rs4715134; hg19: chr6-49488287;