rs9473582

Variant names:

• chr6-49521195-A-C
• rs9473582
• NM_001010904.2:c.314-450A>C

Your query was ambiguous. Multiple possible variants found:

• chr6-49521195-A-C
• chr6-49521195-A-T

Variant summary

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

The NM_001010904.2(GLYATL3):​c.314-450A>C 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 151,862 control chromosomes in the GnomAD database, including 17,251 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 (17251 hom., cov: 32)
• Consequence: GLYATL3 NM_001010904.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.461
• Publications: 9 publications found

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

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• 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 rank	MANE	Protein	UniProt
GLYATL3	NM_001010904.2	c.314-450A>C		intron_variant	Intron 4 of 5	ENST00000371197.9	NP_001010904.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GLYATL3	ENST00000371197.9	c.314-450A>C		intron_variant	Intron 4 of 5	2	NM_001010904.2	ENSP00000360240.4
GLYATL3	ENST00000545705.1	c.314-450A>C		intron_variant	Intron 4 of 5	5		ENSP00000440029.1

Frequencies

GnomAD3 genomes AF: 0.465 AC: 70546 AN: 151744 Hom.: 17231 Cov.: 32

Gnomad AFR AF: 0.554

Gnomad AMI AF: 0.479

Gnomad AMR AF: 0.578

Gnomad ASJ AF: 0.376

Gnomad EAS AF: 0.618

Gnomad SAS AF: 0.474

Gnomad FIN AF: 0.479

Gnomad MID AF: 0.459

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: 70612 AN: 151862 Hom.: 17251 Cov.: 32 AF XY: 0.475 AC XY: 35254 AN XY: 74210

African (AFR) AF: 0.554 AC: 22941 AN: 41404

American (AMR) AF: 0.578 AC: 8815 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.376 AC: 1304 AN: 3464

East Asian (EAS) AF: 0.618 AC: 3181 AN: 5150

South Asian (SAS) AF: 0.472 AC: 2271 AN: 4808

European-Finnish (FIN) AF: 0.479 AC: 5046 AN: 10544

Middle Eastern (MID) AF: 0.456 AC: 134 AN: 294

European-Non Finnish (NFE) AF: 0.376 AC: 25550 AN: 67938

Other (OTH) AF: 0.443 AC: 934 AN: 2106

Alfa AF: 0.403 Hom.: 28165

Bravo AF: 0.479

Asia WGS AF: 0.559 AC: 1941 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.81
DANN	Benign	0.58
PhyloP100		-0.46
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs9473582; hg19: chr6-49488908;