rs10049088

Variant names:

• chr3-157079859-C-T
• rs10049088
• ENST00000782045.1:n.569-5656G>A

Variant summary

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

The ENST00000782045.1(LINC00880):​n.569-5656G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.357 in 151,734 control chromosomes in the GnomAD database, including 10,159 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 (10159 hom., cov: 31)
• Consequence: LINC00880 ENST00000782045.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.444
• Publications: 24 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=-0.79).
• 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.569-5656G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.358 AC: 54205 AN: 151616 Hom.: 10163 Cov.: 31

Gnomad AFR AF: 0.255

Gnomad AMI AF: 0.404

Gnomad AMR AF: 0.414

Gnomad ASJ AF: 0.501

Gnomad EAS AF: 0.504

Gnomad SAS AF: 0.257

Gnomad FIN AF: 0.309

Gnomad MID AF: 0.449

Gnomad NFE AF: 0.401

Gnomad OTH AF: 0.401

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

GnomAD4 genome AF: 0.357 AC: 54220 AN: 151734 Hom.: 10159 Cov.: 31 AF XY: 0.354 AC XY: 26201 AN XY: 74110

African (AFR) AF: 0.255 AC: 10550 AN: 41334

American (AMR) AF: 0.414 AC: 6316 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.501 AC: 1736 AN: 3468

East Asian (EAS) AF: 0.503 AC: 2591 AN: 5146

South Asian (SAS) AF: 0.257 AC: 1240 AN: 4826

European-Finnish (FIN) AF: 0.309 AC: 3233 AN: 10472

Middle Eastern (MID) AF: 0.432 AC: 127 AN: 294

European-Non Finnish (NFE) AF: 0.401 AC: 27226 AN: 67930

Other (OTH) AF: 0.399 AC: 833 AN: 2090

Alfa AF: 0.389 Hom.: 3996

Bravo AF: 0.364

Asia WGS AF: 0.354 AC: 1228 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	6.8
DANN	Benign	0.73
PhyloP100		0.44

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: rs10049088;

hg19: chr3-156797648;