rs12779447

chr10-6322791-G-A

Variant summary

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

The ENST00000659311.1(LINC02649):n.100-3755G>A variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.142 in 152,202 control chromosomes in the GnomAD database, including 1,651 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 0.14 (1651 hom., cov: 32)
• Consequence: LINC02649 ENST00000659311.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00800

Genes affected

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

PFKFB3 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.18 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PFKFB3	XM_047425341.1	c.1456-3755G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC02649	ENST00000659311.1	n.100-3755G>A		intron_variant, non_coding_transcript_variant
LINC02649	ENST00000399868.2	n.122-3755G>A		intron_variant, non_coding_transcript_variant		2
LINC02649	ENST00000670683.1	n.91-3755G>A		intron_variant, non_coding_transcript_variant
LINC02649	ENST00000689295.1	n.81-3755G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.142 AC: 21606 AN: 152084 Hom.: 1652 Cov.: 32

Gnomad AFR AF: 0.112

Gnomad AMI AF: 0.0724

Gnomad AMR AF: 0.107

Gnomad ASJ AF: 0.154

Gnomad EAS AF: 0.0167

Gnomad SAS AF: 0.0815

Gnomad FIN AF: 0.143

Gnomad MID AF: 0.117

Gnomad NFE AF: 0.183

Gnomad OTH AF: 0.122

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

GnomAD4 genome AF: 0.142 AC: 21607 AN: 152202 Hom.: 1651 Cov.: 32 AF XY: 0.138 AC XY: 10287 AN XY: 74412

Gnomad4 AFR AF: 0.112

Gnomad4 AMR AF: 0.107

Gnomad4 ASJ AF: 0.154

Gnomad4 EAS AF: 0.0168

Gnomad4 SAS AF: 0.0812

Gnomad4 FIN AF: 0.143

Gnomad4 NFE AF: 0.183

Gnomad4 OTH AF: 0.120

Alfa AF: 0.167 Hom.: 3026

Bravo AF: 0.137

Asia WGS AF: 0.0570 AC: 200 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
Cadd	Benign	0.89
Dann	Benign	0.75

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12779447; hg19: chr10-6364754;