3-157079913-G-A

Variant names:

• chr3-157079913-G-A
• rs10049090
• ENST00000782045.1:n.569-5710C>T

Variant summary

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

The ENST00000782045.1(LINC00880):​n.569-5710C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.463 in 151,958 control chromosomes in the GnomAD database, including 16,782 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 0.46 (16782 hom., cov: 32)
• Consequence: LINC00880 ENST00000782045.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.836
• Publications: 13 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=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.627 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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC00880	ENST00000782045.1		n.569-5710C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.463 AC: 70370 AN: 151840 Hom.: 16766 Cov.: 32

Gnomad AFR AF: 0.534

Gnomad AMI AF: 0.405

Gnomad AMR AF: 0.463

Gnomad ASJ AF: 0.554

Gnomad EAS AF: 0.645

Gnomad SAS AF: 0.527

Gnomad FIN AF: 0.328

Gnomad MID AF: 0.579

Gnomad NFE AF: 0.418

Gnomad OTH AF: 0.498

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

GnomAD4 genome AF: 0.463 AC: 70423 AN: 151958 Hom.: 16782 Cov.: 32 AF XY: 0.462 AC XY: 34290 AN XY: 74272

African (AFR) AF: 0.534 AC: 22135 AN: 41418

American (AMR) AF: 0.463 AC: 7066 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.554 AC: 1923 AN: 3468

East Asian (EAS) AF: 0.646 AC: 3336 AN: 5168

South Asian (SAS) AF: 0.525 AC: 2528 AN: 4818

European-Finnish (FIN) AF: 0.328 AC: 3463 AN: 10560

Middle Eastern (MID) AF: 0.568 AC: 167 AN: 294

European-Non Finnish (NFE) AF: 0.418 AC: 28395 AN: 67946

Other (OTH) AF: 0.495 AC: 1041 AN: 2102

Alfa AF: 0.462 Hom.: 5839

Bravo AF: 0.476

Asia WGS AF: 0.565 AC: 1966 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.50
DANN	Benign	0.57
PhyloP100		-0.84

Splicing

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

Other links and lift over

dbSNP: rs10049090; hg19: chr3-156797702;