rs1648180

chr11-128179507-A-G

Variant summary

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

The NR_183639.1(LINC02725):n.703-953A>G 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 0.635 in 152,038 control chromosomes in the GnomAD database, including 32,458 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 0.63 (32458 hom., cov: 32)
• Consequence: LINC02725 NR_183639.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.336

Genes affected

LINC02725 (HGNC:54242): (long intergenic non-protein coding RNA 2725)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.7).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.733 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC02725	NR_183639.1	n.703-953A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC02725	ENST00000664091.1	n.485-953A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.635 AC: 96511 AN: 151918 Hom.: 32452 Cov.: 32

Gnomad AFR AF: 0.570

Gnomad AMI AF: 0.730

Gnomad AMR AF: 0.474

Gnomad ASJ AF: 0.738

Gnomad EAS AF: 0.0404

Gnomad SAS AF: 0.546

Gnomad FIN AF: 0.747

Gnomad MID AF: 0.677

Gnomad NFE AF: 0.739

Gnomad OTH AF: 0.642

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

GnomAD4 genome AF: 0.635 AC: 96542 AN: 152038 Hom.: 32458 Cov.: 32 AF XY: 0.628 AC XY: 46636 AN XY: 74308

Gnomad4 AFR AF: 0.569

Gnomad4 AMR AF: 0.473

Gnomad4 ASJ AF: 0.738

Gnomad4 EAS AF: 0.0407

Gnomad4 SAS AF: 0.547

Gnomad4 FIN AF: 0.747

Gnomad4 NFE AF: 0.739

Gnomad4 OTH AF: 0.638

Alfa AF: 0.708 Hom.: 51029

Bravo AF: 0.609

Asia WGS AF: 0.339 AC: 1180 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.70
Cadd	Benign	2.8
Dann	Benign	0.84

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1648180; hg19: chr11-128049402;