rs11773340

Positions:

• chr7-141617034-C-T

Variant summary

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

The NM_018238.4(AGK):​c.518+1469C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.377 in 151,872 control chromosomes in the GnomAD database, including 11,717 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 0.38 (11717 hom., cov: 31)
• Consequence: AGK NM_018238.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.394

Genes affected

AGK (HGNC:21869): (acylglycerol kinase) The protein encoded by this gene is a mitochondrial membrane protein involved in lipid and glycerolipid metabolism. The encoded protein is a lipid kinase that catalyzes the formation of phosphatidic and lysophosphatidic acids. Defects in this gene have been associated with mitochondrial DNA depletion syndrome 10. [provided by RefSeq, Feb 2012]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.524 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
AGK	NM_018238.4	c.518+1469C>T		intron_variant		ENST00000649286.2
AGK	NM_001364948.3	c.518+1469C>T		intron_variant
AGK	XM_011516397.4	c.518+1469C>T		intron_variant
AGK	XM_024446835.2	c.518+1469C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
AGK	ENST00000649286.2	c.518+1469C>T		intron_variant			NM_018238.4	P1

Frequencies

GnomAD3 genomes AF: 0.377 AC: 57237 AN: 151752 Hom.: 11710 Cov.: 31

Gnomad AFR AF: 0.206

Gnomad AMI AF: 0.399

Gnomad AMR AF: 0.490

Gnomad ASJ AF: 0.390

Gnomad EAS AF: 0.540

Gnomad SAS AF: 0.369

Gnomad FIN AF: 0.447

Gnomad MID AF: 0.369

Gnomad NFE AF: 0.431

Gnomad OTH AF: 0.410

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

GnomAD4 genome AF: 0.377 AC: 57259 AN: 151872 Hom.: 11717 Cov.: 31 AF XY: 0.381 AC XY: 28238 AN XY: 74204

Gnomad4 AFR AF: 0.206

Gnomad4 AMR AF: 0.490

Gnomad4 ASJ AF: 0.390

Gnomad4 EAS AF: 0.540

Gnomad4 SAS AF: 0.370

Gnomad4 FIN AF: 0.447

Gnomad4 NFE AF: 0.431

Gnomad4 OTH AF: 0.416

Alfa AF: 0.428 Hom.: 14003

Bravo AF: 0.377

Asia WGS AF: 0.434 AC: 1510 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	5.6
DANN	Benign	0.86

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: rs11773340; hg19: chr7-141316834;