ENST00000513853.5:n.304+124311T>C

Variant names:

• chr11-28866219-T-C
• rs11604366
• ENST00000513853.5:n.304+124311T>C

Variant summary

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

The ENST00000513853.5(LINC02742):​n.304+124311T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.361 in 152,036 control chromosomes in the GnomAD database, including 10,517 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 (10517 hom., cov: 32)
• Consequence: LINC02742 ENST00000513853.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.780

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=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.425 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.304+124311T>C		intron_variant	Intron 2 of 3	3
LINC02742	ENST00000662190.1	n.313-16970T>C		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.361 AC: 54795 AN: 151918 Hom.: 10504 Cov.: 32

Gnomad AFR AF: 0.247

Gnomad AMI AF: 0.553

Gnomad AMR AF: 0.410

Gnomad ASJ AF: 0.402

Gnomad EAS AF: 0.340

Gnomad SAS AF: 0.277

Gnomad FIN AF: 0.302

Gnomad MID AF: 0.351

Gnomad NFE AF: 0.430

Gnomad OTH AF: 0.403

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

GnomAD4 genome AF: 0.361 AC: 54850 AN: 152036 Hom.: 10517 Cov.: 32 AF XY: 0.353 AC XY: 26263 AN XY: 74310

Gnomad4 AFR AF: 0.247

Gnomad4 AMR AF: 0.410

Gnomad4 ASJ AF: 0.402

Gnomad4 EAS AF: 0.340

Gnomad4 SAS AF: 0.276

Gnomad4 FIN AF: 0.302

Gnomad4 NFE AF: 0.430

Gnomad4 OTH AF: 0.408

Alfa AF: 0.424 Hom.: 28696

Bravo AF: 0.370

Asia WGS AF: 0.350 AC: 1220 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.87
DANN	Benign	0.79

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11604366; hg19: chr11-28887766;