3-142206197-T-C

Position:

• chr3-142206197-T-C

Variant summary

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

The NM_001039547.3(GK5):​c.318-1409A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.708 in 152,110 control chromosomes in the GnomAD database, including 38,744 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 0.71 (38744 hom., cov: 32)
• Consequence: GK5 NM_001039547.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.257

Genes affected

GK5 (HGNC:28635): (glycerol kinase 5) Predicted to enable glycerol kinase activity. Predicted to be involved in several processes, including glycerol metabolic process; glycerol-3-phosphate biosynthetic process; and triglyceride metabolic process. Predicted to be active 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=-1.03).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.813 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
GK5	NM_001039547.3	c.318-1409A>G		intron_variant		ENST00000392993.7	NP_001034636.1
GK5	XM_047447897.1	c.318-1409A>G		intron_variant			XP_047303853.1
GK5	NR_033289.2	n.448-1409A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
GK5	ENST00000392993.7	c.318-1409A>G		intron_variant		1	NM_001039547.3	ENSP00000418001	P1

Frequencies

GnomAD3 genomes AF: 0.708 AC: 107612 AN: 151992 Hom.: 38686 Cov.: 32

Gnomad AFR AF: 0.820

Gnomad AMI AF: 0.809

Gnomad AMR AF: 0.693

Gnomad ASJ AF: 0.734

Gnomad EAS AF: 0.522

Gnomad SAS AF: 0.463

Gnomad FIN AF: 0.692

Gnomad MID AF: 0.712

Gnomad NFE AF: 0.674

Gnomad OTH AF: 0.702

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

GnomAD4 genome AF: 0.708 AC: 107724 AN: 152110 Hom.: 38744 Cov.: 32 AF XY: 0.705 AC XY: 52456 AN XY: 74378

Gnomad4 AFR AF: 0.821

Gnomad4 AMR AF: 0.693

Gnomad4 ASJ AF: 0.734

Gnomad4 EAS AF: 0.521

Gnomad4 SAS AF: 0.462

Gnomad4 FIN AF: 0.692

Gnomad4 NFE AF: 0.674

Gnomad4 OTH AF: 0.707

Alfa AF: 0.687 Hom.: 34877

Bravo AF: 0.717

Asia WGS AF: 0.536 AC: 1866 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	3.2
DANN	Benign	0.52

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: rs4485736; hg19: chr3-141925039;