rs10501109

chr11-29039573-T-Cchr11-29039573-T-G

Variant summary

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

The NR_183752.1(LINC02742):n.208+1757T>C variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0279 in 152,184 control chromosomes in the GnomAD database, including 256 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 (256 hom., cov: 32)
• Consequence: LINC02742 NR_183752.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.581

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=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.204 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC02742	NR_183752.1	n.208+1757T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC02742	ENST00000513853.5	n.379+1757T>C		intron_variant, non_coding_transcript_variant		3
LINC02742	ENST00000511073.2	n.198+1757T>C		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.0278 AC: 4233 AN: 152066 Hom.: 256 Cov.: 32

Gnomad AFR AF: 0.00645

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.111

Gnomad ASJ AF: 0.0260

Gnomad EAS AF: 0.215

Gnomad SAS AF: 0.0147

Gnomad FIN AF: 0.0107

Gnomad MID AF: 0.0158

Gnomad NFE AF: 0.0120

Gnomad OTH AF: 0.0335

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

GnomAD4 genome AF: 0.0279 AC: 4239 AN: 152184 Hom.: 256 Cov.: 32 AF XY: 0.0301 AC XY: 2242 AN XY: 74416

Gnomad4 AFR AF: 0.00650

Gnomad4 AMR AF: 0.111

Gnomad4 ASJ AF: 0.0260

Gnomad4 EAS AF: 0.214

Gnomad4 SAS AF: 0.0143

Gnomad4 FIN AF: 0.0107

Gnomad4 NFE AF: 0.0120

Gnomad4 OTH AF: 0.0322

Alfa AF: 0.00515 Hom.: 1

Bravo AF: 0.0350

Asia WGS AF: 0.0900 AC: 312 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	0.077
Dann	Benign	0.44

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10501109; hg19: chr11-29061120;