rs7928853

chr11-29008009-G-C

Variant summary

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

The NR_183752.1(LINC02742):n.134-29733G>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 0.867 in 152,114 control chromosomes in the GnomAD database, including 58,329 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 0.87 (58329 hom., cov: 32)
• Consequence: LINC02742 NR_183752.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.209

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=-1.03).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.961 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC02742	NR_183752.1	n.134-29733G>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC02742	ENST00000513853.5	n.305-29733G>C		intron_variant, non_coding_transcript_variant		3
LINC02742	ENST00000511073.2	n.124-29733G>C		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.867 AC: 131795 AN: 151994 Hom.: 58309 Cov.: 32

Gnomad AFR AF: 0.685

Gnomad AMI AF: 0.993

Gnomad AMR AF: 0.844

Gnomad ASJ AF: 0.967

Gnomad EAS AF: 0.784

Gnomad SAS AF: 0.985

Gnomad FIN AF: 0.906

Gnomad MID AF: 0.975

Gnomad NFE AF: 0.967

Gnomad OTH AF: 0.884

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

GnomAD4 genome AF: 0.867 AC: 131859 AN: 152114 Hom.: 58329 Cov.: 32 AF XY: 0.867 AC XY: 64449 AN XY: 74364

Gnomad4 AFR AF: 0.684

Gnomad4 AMR AF: 0.843

Gnomad4 ASJ AF: 0.967

Gnomad4 EAS AF: 0.784

Gnomad4 SAS AF: 0.985

Gnomad4 FIN AF: 0.906

Gnomad4 NFE AF: 0.967

Gnomad4 OTH AF: 0.886

Alfa AF: 0.912 Hom.: 7939

Bravo AF: 0.853

Asia WGS AF: 0.893 AC: 3107 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	0.39
Dann	Benign	0.42

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7928853; hg19: chr11-29029556;