rs900399

Variant names:

• chr3-157080943-A-G
• rs900399
• ENST00000782045.1:n.569-6740T>C

Variant summary

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

The ENST00000782045.1(LINC00880):​n.569-6740T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.365 in 152,160 control chromosomes in the GnomAD database, including 10,619 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 (10619 hom., cov: 33)
• Consequence: LINC00880 ENST00000782045.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.278
• Publications: 25 publications found

Genes affected

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

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.54).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.487 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

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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC00880	ENST00000782045.1		n.569-6740T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.365 AC: 55471 AN: 152040 Hom.: 10623 Cov.: 33

Gnomad AFR AF: 0.262

Gnomad AMI AF: 0.404

Gnomad AMR AF: 0.423

Gnomad ASJ AF: 0.507

Gnomad EAS AF: 0.504

Gnomad SAS AF: 0.259

Gnomad FIN AF: 0.312

Gnomad MID AF: 0.455

Gnomad NFE AF: 0.410

Gnomad OTH AF: 0.411

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

GnomAD4 genome AF: 0.365 AC: 55488 AN: 152160 Hom.: 10619 Cov.: 33 AF XY: 0.360 AC XY: 26806 AN XY: 74386

African (AFR) AF: 0.262 AC: 10873 AN: 41532

American (AMR) AF: 0.423 AC: 6461 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.507 AC: 1758 AN: 3470

East Asian (EAS) AF: 0.503 AC: 2609 AN: 5184

South Asian (SAS) AF: 0.258 AC: 1248 AN: 4830

European-Finnish (FIN) AF: 0.312 AC: 3298 AN: 10574

Middle Eastern (MID) AF: 0.446 AC: 131 AN: 294

European-Non Finnish (NFE) AF: 0.410 AC: 27880 AN: 67960

Other (OTH) AF: 0.408 AC: 862 AN: 2114

Alfa AF: 0.404 Hom.: 40258

Bravo AF: 0.372

Asia WGS AF: 0.353 AC: 1224 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.54
CADD	Benign	8.0
DANN	Benign	0.84
PhyloP100		-0.28

Splicing

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

Other links and lift over

dbSNP: rs900399; hg19: chr3-156798732;