rs900400

Variant names:

• chr3-157080986-T-C
• rs900400
• ENST00000782045.1:n.569-6783A>G

Your query was ambiguous. Multiple possible variants found:

• chr3-157080986-T-C
• chr3-157080986-T-G

Variant summary

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

The ENST00000782045.1(LINC00880):​n.569-6783A>G 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 152,188 control chromosomes in the GnomAD database, including 10,667 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 0.37 (10667 hom., cov: 33)
• Consequence: LINC00880 ENST00000782045.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.106
• Publications: 64 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=-0.68).
• 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

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.569-6783A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.365 AC: 55574 AN: 152070 Hom.: 10672 Cov.: 33

Gnomad AFR AF: 0.262

Gnomad AMI AF: 0.404

Gnomad AMR AF: 0.424

Gnomad ASJ AF: 0.513

Gnomad EAS AF: 0.504

Gnomad SAS AF: 0.259

Gnomad FIN AF: 0.312

Gnomad MID AF: 0.459

Gnomad NFE AF: 0.411

Gnomad OTH AF: 0.412

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

GnomAD4 genome AF: 0.365 AC: 55589 AN: 152188 Hom.: 10667 Cov.: 33 AF XY: 0.361 AC XY: 26841 AN XY: 74408

African (AFR) AF: 0.262 AC: 10885 AN: 41548

American (AMR) AF: 0.424 AC: 6479 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.513 AC: 1779 AN: 3468

East Asian (EAS) AF: 0.503 AC: 2608 AN: 5182

South Asian (SAS) AF: 0.258 AC: 1247 AN: 4824

European-Finnish (FIN) AF: 0.312 AC: 3304 AN: 10582

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

European-Non Finnish (NFE) AF: 0.411 AC: 27923 AN: 67982

Other (OTH) AF: 0.409 AC: 865 AN: 2114

Alfa AF: 0.403 Hom.: 24509

Bravo AF: 0.373

Asia WGS AF: 0.354 AC: 1226 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.68
CADD	Benign	3.5
DANN	Benign	0.88
PhyloP100		-0.11

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: rs900400;

hg19: chr3-156798775;