rs1648180

Variant names:

• chr11-128179507-A-G
• rs1648180
• ENST00000671140.1:n.738A>G

Variant summary

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

The ENST00000671140.1(LINC02725):​n.738A>G variant causes a non coding transcript exon 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 ENST00000671140.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.336
• Publications: 3 publications found

Genes affected

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

ENSG00000301990 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
LINC02725	NR_183639.1	n.703-953A>G		intron_variant	Intron 4 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02725	ENST00000671140.1	n.738A>G		non_coding_transcript_exon_variant	Exon 5 of 7
LINC02725	ENST00000649115.1	n.1009-953A>G		intron_variant	Intron 7 of 8
LINC02725	ENST00000654938.1	n.1103-953A>G		intron_variant	Intron 6 of 7

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

African (AFR) AF: 0.569 AC: 23592 AN: 41432

American (AMR) AF: 0.473 AC: 7229 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.738 AC: 2561 AN: 3468

East Asian (EAS) AF: 0.0407 AC: 211 AN: 5184

South Asian (SAS) AF: 0.547 AC: 2636 AN: 4822

European-Finnish (FIN) AF: 0.747 AC: 7881 AN: 10554

Middle Eastern (MID) AF: 0.680 AC: 200 AN: 294

European-Non Finnish (NFE) AF: 0.739 AC: 50220 AN: 67988

Other (OTH) AF: 0.638 AC: 1348 AN: 2114

Alfa AF: 0.700 Hom.: 63590

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
PhyloP100		-0.34

Splicing

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

Other links and lift over

dbSNP: rs1648180; hg19: chr11-128049402;