rs10875746

chr12-48124481-A-C

Variant summary

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

The NM_000289.6(PFKM):c.85+1622A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.211 in 152,144 control chromosomes in the GnomAD database, including 3,536 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 0.21 (3536 hom., cov: 32)
• Consequence: PFKM NM_000289.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.259

Genes affected

PFKM (HGNC:8877): (phosphofructokinase, muscle) Three phosphofructokinase isozymes exist in humans: muscle, liver and platelet. These isozymes function as subunits of the mammalian tetramer phosphofructokinase, which catalyzes the phosphorylation of fructose-6-phosphate to fructose-1,6-bisphosphate. Tetramer composition varies depending on tissue type. This gene encodes the muscle-type isozyme. Mutations in this gene have been associated with glycogen storage disease type VII, also known as Tarui disease. Alternatively spliced transcript variants have been described.[provided by RefSeq, Nov 2009]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.231 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PFKM	NM_000289.6	c.85+1622A>C		intron_variant		ENST00000359794.11

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PFKM	ENST00000359794.11	c.85+1622A>C		intron_variant		1	NM_000289.6	P1

Frequencies

GnomAD3 genomes AF: 0.212 AC: 32155 AN: 152026 Hom.: 3533 Cov.: 32

Gnomad AFR AF: 0.195

Gnomad AMI AF: 0.151

Gnomad AMR AF: 0.205

Gnomad ASJ AF: 0.320

Gnomad EAS AF: 0.242

Gnomad SAS AF: 0.147

Gnomad FIN AF: 0.132

Gnomad MID AF: 0.237

Gnomad NFE AF: 0.232

Gnomad OTH AF: 0.241

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

GnomAD4 genome AF: 0.211 AC: 32178 AN: 152144 Hom.: 3536 Cov.: 32 AF XY: 0.207 AC XY: 15373 AN XY: 74400

Gnomad4 AFR AF: 0.195

Gnomad4 AMR AF: 0.205

Gnomad4 ASJ AF: 0.320

Gnomad4 EAS AF: 0.242

Gnomad4 SAS AF: 0.146

Gnomad4 FIN AF: 0.132

Gnomad4 NFE AF: 0.232

Gnomad4 OTH AF: 0.239

Alfa AF: 0.217 Hom.: 1931

Bravo AF: 0.218

Asia WGS AF: 0.161 AC: 560 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	1.5
Dann	Benign	0.58

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: rs10875746; hg19: chr12-48518264;