rs4485736

Variant names:

• chr3-142206197-T-C
• rs4485736
• NM_001039547.3:c.318-1409A>G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 6 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001039547.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GK5	NM_001039547.3	MANE Select	c.318-1409A>G		intron	N/A	NP_001034636.1
	GK5	NR_033289.2		n.448-1409A>G		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GK5	ENST00000392993.7	TSL:1 MANE Select	c.318-1409A>G		intron	N/A	ENSP00000418001.1
	GK5	ENST00000480757.5	TSL:1	n.318-1409A>G		intron	N/A	ENSP00000419031.1
	GK5	ENST00000487672.1	TSL:1	n.318-1409A>G		intron	N/A	ENSP00000418239.1

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

African (AFR) AF: 0.821 AC: 34067 AN: 41512

American (AMR) AF: 0.693 AC: 10596 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.734 AC: 2548 AN: 3472

East Asian (EAS) AF: 0.521 AC: 2690 AN: 5162

South Asian (SAS) AF: 0.462 AC: 2230 AN: 4822

European-Finnish (FIN) AF: 0.692 AC: 7325 AN: 10578

Middle Eastern (MID) AF: 0.707 AC: 205 AN: 290

European-Non Finnish (NFE) AF: 0.674 AC: 45834 AN: 67966

Other (OTH) AF: 0.707 AC: 1491 AN: 2108

Alfa AF: 0.692 Hom.: 44633

Bravo AF: 0.717

Asia WGS AF: 0.536 AC: 1866 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	3.2
DANN	Benign	0.52
PhyloP100		-0.26
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: rs4485736; hg19: chr3-141925039;