rs41393946

Variant names:

• chr11-28996017-G-A
• rs41393946
• ENST00000511073.2:n.124-41725G>A

Variant summary

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

The ENST00000511073.2(LINC02742):​n.124-41725G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0278 in 152,122 control chromosomes in the GnomAD database, including 263 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 0.028 (263 hom., cov: 32)
• Consequence: LINC02742 ENST00000511073.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.282
• Publications: 1 publications found

Genes affected

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

ENSG00000302619 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.205 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02742	NR_183752.1	n.134-41725G>A		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02742	ENST00000511073.2	n.124-41725G>A		intron_variant	Intron 1 of 3	3
LINC02742	ENST00000513853.6	n.305-41725G>A		intron_variant	Intron 2 of 3	3
LINC02742	ENST00000788053.1	n.259-41725G>A		intron_variant	Intron 2 of 4

Frequencies

GnomAD3 genomes AF: 0.0277 AC: 4212 AN: 152004 Hom.: 260 Cov.: 32

Gnomad AFR AF: 0.0304

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.104

Gnomad ASJ AF: 0.00288

Gnomad EAS AF: 0.216

Gnomad SAS AF: 0.0207

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00316

Gnomad NFE AF: 0.00129

Gnomad OTH AF: 0.0301

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

GnomAD4 genome AF: 0.0278 AC: 4225 AN: 152122 Hom.: 263 Cov.: 32 AF XY: 0.0305 AC XY: 2266 AN XY: 74358

African (AFR) AF: 0.0305 AC: 1267 AN: 41524

American (AMR) AF: 0.104 AC: 1593 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.00288 AC: 10 AN: 3468

East Asian (EAS) AF: 0.215 AC: 1106 AN: 5138

South Asian (SAS) AF: 0.0201 AC: 97 AN: 4820

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 10612

Middle Eastern (MID) AF: 0.0102 AC: 3 AN: 294

European-Non Finnish (NFE) AF: 0.00129 AC: 88 AN: 67996

Other (OTH) AF: 0.0289 AC: 61 AN: 2112

Alfa AF: 0.0161 Hom.: 18

Bravo AF: 0.0360

Asia WGS AF: 0.0910 AC: 314 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	7.8
DANN	Benign	0.76
PhyloP100		0.28

Splicing

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

Other links and lift over

dbSNP: rs41393946; hg19: chr11-29017564;