chr7-141551244-C-G

Position:

• chr7-141551244-C-G

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_Strong BP6_Very_Strong BA1

The NR_183408.1(AGK-DT):​n.101G>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0925 in 152,302 control chromosomes in the GnomAD database, including 1,420 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency:
  • Genomes: 𝑓 0.092 (1420 hom., cov: 32)
  • Exomes 𝑓: 0.043 (0 hom.)
• Consequence: AGK-DT NR_183408.1 non_coding_transcript_exon
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: -3.19

Genes affected

AGK-DT (HGNC:55356): (AGK divergent transcript)

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 -20 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BP6: Variant 7-141551244-C-G is Benign according to our data. Variant chr7-141551244-C-G is described in ClinVar as [Benign]. Clinvar id is 1329639.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.245 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
AGK-DT	NR_183408.1	n.101G>C		non_coding_transcript_exon_variant	1/6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
AGK-DT	ENST00000567503.1	n.61G>C		non_coding_transcript_exon_variant	1/4	3
AGK-DT	ENST00000668372.1	n.29G>C		non_coding_transcript_exon_variant	1/3
AGK	ENST00000629555.2			upstream_gene_variant		5

Frequencies

GnomAD3 genomes AF: 0.0921 AC: 14019 AN: 152140 Hom.: 1410 Cov.: 32

Gnomad AFR AF: 0.249

Gnomad AMI AF: 0.00329

Gnomad AMR AF: 0.0442

Gnomad ASJ AF: 0.0190

Gnomad EAS AF: 0.0385

Gnomad SAS AF: 0.149

Gnomad FIN AF: 0.0127

Gnomad MID AF: 0.0285

Gnomad NFE AF: 0.0258

Gnomad OTH AF: 0.0740

GnomAD4 exome AF: 0.0435 AC: 2 AN: 46 Hom.: 0 Cov.: 0 AF XY: 0.0250 AC XY: 1 AN XY: 40

Gnomad4 AFR exome AF: 0.500

Gnomad4 EAS exome AF: 0.00

Gnomad4 NFE exome AF: 0.0263

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.0925 AC: 14080 AN: 152256 Hom.: 1420 Cov.: 32 AF XY: 0.0915 AC XY: 6809 AN XY: 74444

Gnomad4 AFR AF: 0.249

Gnomad4 AMR AF: 0.0444

Gnomad4 ASJ AF: 0.0190

Gnomad4 EAS AF: 0.0386

Gnomad4 SAS AF: 0.150

Gnomad4 FIN AF: 0.0127

Gnomad4 NFE AF: 0.0258

Gnomad4 OTH AF: 0.0742

Alfa AF: 0.0626 Hom.: 95

Bravo AF: 0.100

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

not provided Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Dec 21, 2021	- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.2
DANN	Benign	0.56

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: rs7795885; hg19: chr7-141251044;