ENST00000782045.1:n.569-5617A>G

Variant names:

• chr3-157079820-T-C
• rs17451107
• ENST00000782045.1:n.569-5617A>G

Variant summary

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

The ENST00000782045.1(LINC00880):​n.569-5617A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.382 in 151,932 control chromosomes in the GnomAD database, including 11,306 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 0.38 (11306 hom., cov: 32)
• Consequence: LINC00880 ENST00000782045.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.87
• Publications: 51 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=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.487 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC00880	ENST00000782045.1	n.569-5617A>G		intron_variant	Intron 4 of 4

Frequencies

GnomAD3 genomes AF: 0.382 AC: 57941 AN: 151814 Hom.: 11305 Cov.: 32

Gnomad AFR AF: 0.339

Gnomad AMI AF: 0.404

Gnomad AMR AF: 0.421

Gnomad ASJ AF: 0.502

Gnomad EAS AF: 0.504

Gnomad SAS AF: 0.257

Gnomad FIN AF: 0.308

Gnomad MID AF: 0.456

Gnomad NFE AF: 0.402

Gnomad OTH AF: 0.419

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

GnomAD4 genome AF: 0.382 AC: 57974 AN: 151932 Hom.: 11306 Cov.: 32 AF XY: 0.376 AC XY: 27946 AN XY: 74272

African (AFR) AF: 0.339 AC: 14046 AN: 41408

American (AMR) AF: 0.421 AC: 6419 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.502 AC: 1743 AN: 3470

East Asian (EAS) AF: 0.503 AC: 2599 AN: 5162

South Asian (SAS) AF: 0.257 AC: 1237 AN: 4818

European-Finnish (FIN) AF: 0.308 AC: 3250 AN: 10538

Middle Eastern (MID) AF: 0.439 AC: 129 AN: 294

European-Non Finnish (NFE) AF: 0.402 AC: 27307 AN: 67960

Other (OTH) AF: 0.416 AC: 876 AN: 2108

Alfa AF: 0.401 Hom.: 46593

Bravo AF: 0.392

Asia WGS AF: 0.361 AC: 1253 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.42
DANN	Benign	0.53
PhyloP100		-1.9

Splicing

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

Other links and lift over

dbSNP: rs17451107; hg19: chr3-156797609;