rs7077335

Variant names:

• chr10-6273831-C-A
• rs7077335
• XM_047425341.1:c.1455+47466C>A

Your query was ambiguous. Multiple possible variants found:

• chr10-6273831-C-A
• chr10-6273831-C-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000659311.1(LINC02649):​n.99+2564C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.842 in 152,154 control chromosomes in the GnomAD database, including 57,314 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 0.84 (57314 hom., cov: 31)
• Consequence: LINC02649 ENST00000659311.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.92
• Publications: 8 publications found

Genes affected

PFKFB3 (HGNC:8874): (6-phosphofructo-2-kinase/fructose-2,6-biphosphatase 3) The protein encoded by this gene belongs to a family of bifunctional proteins that are involved in both the synthesis and degradation of fructose-2,6-bisphosphate, a regulatory molecule that controls glycolysis in eukaryotes. The encoded protein has a 6-phosphofructo-2-kinase activity that catalyzes the synthesis of fructose-2,6-bisphosphate (F2,6BP), and a fructose-2,6-biphosphatase activity that catalyzes the degradation of F2,6BP. This protein is required for cell cycle progression and prevention of apoptosis. It functions as a regulator of cyclin-dependent kinase 1, linking glucose metabolism to cell proliferation and survival in tumor cells. Several alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Apr 2016]

LINC02649 (HGNC:54134): (long intergenic non-protein coding RNA 2649)

ENSG00000302099 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.981 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000659311.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02649	ENST00000659311.1		n.99+2564C>A		intron	N/A
	LINC02649	ENST00000689295.1		n.80+2564C>A		intron	N/A
	LINC02649	ENST00000783921.1		n.70+2564C>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.843 AC: 128105 AN: 152036 Hom.: 57301 Cov.: 31

Gnomad AFR AF: 0.512

Gnomad AMI AF: 0.993

Gnomad AMR AF: 0.904

Gnomad ASJ AF: 0.961

Gnomad EAS AF: 0.817

Gnomad SAS AF: 0.990

Gnomad FIN AF: 0.995

Gnomad MID AF: 0.946

Gnomad NFE AF: 0.987

Gnomad OTH AF: 0.899

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

GnomAD4 genome AF: 0.842 AC: 128157 AN: 152154 Hom.: 57314 Cov.: 31 AF XY: 0.848 AC XY: 63058 AN XY: 74380

African (AFR) AF: 0.512 AC: 21211 AN: 41442

American (AMR) AF: 0.904 AC: 13810 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.961 AC: 3338 AN: 3472

East Asian (EAS) AF: 0.816 AC: 4218 AN: 5166

South Asian (SAS) AF: 0.990 AC: 4773 AN: 4822

European-Finnish (FIN) AF: 0.995 AC: 10571 AN: 10624

Middle Eastern (MID) AF: 0.946 AC: 278 AN: 294

European-Non Finnish (NFE) AF: 0.987 AC: 67152 AN: 68030

Other (OTH) AF: 0.899 AC: 1900 AN: 2114

Alfa AF: 0.944 Hom.: 278211

Bravo AF: 0.819

Asia WGS AF: 0.905 AC: 3148 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	0.075
DANN	Benign	0.39
PhyloP100		-3.9

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs7077335;

hg19: chr10-6315794;