rs2511864

Positions:

• chr11-82808134-A-C

Variant summary

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

The NR_183631.1(LINC02734):​n.202-8630A>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 0.21 in 152,076 control chromosomes in the GnomAD database, including 4,473 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 0.21 (4473 hom., cov: 32)
• Consequence: LINC02734 NR_183631.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.26

Genes affected

LINC02734 (HGNC:54251): (long intergenic non-protein coding RNA 2734)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.493 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC02734	NR_183631.1	n.202-8630A>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC02734	ENST00000657980.1	n.202-8630A>C		intron_variant, non_coding_transcript_variant
LINC02734	ENST00000526305.2	n.231-8630A>C		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.210 AC: 31836 AN: 151958 Hom.: 4452 Cov.: 32

Gnomad AFR AF: 0.358

Gnomad AMI AF: 0.0526

Gnomad AMR AF: 0.174

Gnomad ASJ AF: 0.0818

Gnomad EAS AF: 0.510

Gnomad SAS AF: 0.307

Gnomad FIN AF: 0.116

Gnomad MID AF: 0.231

Gnomad NFE AF: 0.121

Gnomad OTH AF: 0.187

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

GnomAD4 genome AF: 0.210 AC: 31905 AN: 152076 Hom.: 4473 Cov.: 32 AF XY: 0.213 AC XY: 15809 AN XY: 74352

Gnomad4 AFR AF: 0.359

Gnomad4 AMR AF: 0.174

Gnomad4 ASJ AF: 0.0818

Gnomad4 EAS AF: 0.509

Gnomad4 SAS AF: 0.307

Gnomad4 FIN AF: 0.116

Gnomad4 NFE AF: 0.121

Gnomad4 OTH AF: 0.191

Alfa AF: 0.164 Hom.: 414

Bravo AF: 0.218

Asia WGS AF: 0.387 AC: 1345 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.30
DANN	Benign	0.49

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2511864; hg19: chr11-82519176;