rs1482853

Variant names:

• chr3-157080684-C-A
• rs1482853
• ENST00000782045.1:n.569-6481G>T

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000782045.1(LINC00880):​n.569-6481G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.363 in 152,052 control chromosomes in the GnomAD database, including 10,521 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 0.36 (10521 hom., cov: 32)
• Consequence: LINC00880 ENST00000782045.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.395
• Publications: 25 publications found

Genes affected

LINC00880 (HGNC:27948): (long intergenic non-protein coding RNA 880)

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.44).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.485 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000782045.1. 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
	LINC00880	ENST00000782045.1		n.569-6481G>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.363 AC: 55187 AN: 151934 Hom.: 10526 Cov.: 32

Gnomad AFR AF: 0.261

Gnomad AMI AF: 0.404

Gnomad AMR AF: 0.421

Gnomad ASJ AF: 0.507

Gnomad EAS AF: 0.502

Gnomad SAS AF: 0.258

Gnomad FIN AF: 0.309

Gnomad MID AF: 0.455

Gnomad NFE AF: 0.408

Gnomad OTH AF: 0.410

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

GnomAD4 genome AF: 0.363 AC: 55202 AN: 152052 Hom.: 10521 Cov.: 32 AF XY: 0.359 AC XY: 26668 AN XY: 74342

African (AFR) AF: 0.261 AC: 10823 AN: 41454

American (AMR) AF: 0.421 AC: 6435 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.507 AC: 1760 AN: 3472

East Asian (EAS) AF: 0.501 AC: 2592 AN: 5174

South Asian (SAS) AF: 0.258 AC: 1243 AN: 4826

European-Finnish (FIN) AF: 0.309 AC: 3266 AN: 10558

Middle Eastern (MID) AF: 0.442 AC: 129 AN: 292

European-Non Finnish (NFE) AF: 0.408 AC: 27725 AN: 67962

Other (OTH) AF: 0.407 AC: 861 AN: 2114

Alfa AF: 0.396 Hom.: 19607

Bravo AF: 0.371

Asia WGS AF: 0.355 AC: 1231 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.44
CADD	Benign	13
DANN	Benign	0.44
PhyloP100		0.40

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: rs1482853;

hg19: chr3-156798473;