rs1879445

Variant names:

• chr11-28710895-G-A
• rs1879445
• ENST00000513853.5:n.220+8061G>A

Your query was ambiguous. Multiple possible variants found:

• chr11-28710895-G-A
• chr11-28710895-G-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000513853.5(LINC02742):​n.220+8061G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.627 in 151,806 control chromosomes in the GnomAD database, including 30,585 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 0.63 (30585 hom., cov: 30)
• Consequence: LINC02742 ENST00000513853.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0440

Genes affected

LINC02742 (HGNC:54259): (long intergenic non-protein coding RNA 2742)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.881 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
LINC02742	ENST00000513853.5	n.220+8061G>A		intron_variant	Intron 1 of 3	3
LINC02742	ENST00000662190.1	n.228+8061G>A		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.627 AC: 95156 AN: 151688 Hom.: 30564 Cov.: 30

Gnomad AFR AF: 0.504

Gnomad AMI AF: 0.759

Gnomad AMR AF: 0.685

Gnomad ASJ AF: 0.641

Gnomad EAS AF: 0.903

Gnomad SAS AF: 0.487

Gnomad FIN AF: 0.772

Gnomad MID AF: 0.608

Gnomad NFE AF: 0.653

Gnomad OTH AF: 0.636

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

GnomAD4 genome AF: 0.627 AC: 95230 AN: 151806 Hom.: 30585 Cov.: 30 AF XY: 0.631 AC XY: 46795 AN XY: 74188

Gnomad4 AFR AF: 0.504

Gnomad4 AMR AF: 0.685

Gnomad4 ASJ AF: 0.641

Gnomad4 EAS AF: 0.903

Gnomad4 SAS AF: 0.489

Gnomad4 FIN AF: 0.772

Gnomad4 NFE AF: 0.653

Gnomad4 OTH AF: 0.638

Alfa AF: 0.650 Hom.: 42211

Bravo AF: 0.623

Asia WGS AF: 0.700 AC: 2437 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.2
DANN	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1879445; hg19: chr11-28732442;