11-135072732-A-G

Position:

• chr11-135072732-A-G

Variant summary

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

The NR_183661.1(LINC02684):​n.1690T>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.582 in 151,986 control chromosomes in the GnomAD database, including 26,640 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 0.58 (26640 hom., cov: 32)
• Consequence: LINC02684 NR_183661.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.75

Genes affected

LINC02684 (HGNC:54180): (long intergenic non-protein coding RNA 2684)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.731 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC02684	NR_183661.1	n.1690T>C		non_coding_transcript_exon_variant	3/3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC02684	ENST00000657926.1	n.1401T>C		non_coding_transcript_exon_variant	3/3
LINC02684	ENST00000532071.1	n.547+1382T>C		intron_variant		3

Frequencies

GnomAD3 genomes AF: 0.582 AC: 88406 AN: 151868 Hom.: 26607 Cov.: 32

Gnomad AFR AF: 0.738

Gnomad AMI AF: 0.578

Gnomad AMR AF: 0.593

Gnomad ASJ AF: 0.514

Gnomad EAS AF: 0.690

Gnomad SAS AF: 0.470

Gnomad FIN AF: 0.510

Gnomad MID AF: 0.535

Gnomad NFE AF: 0.500

Gnomad OTH AF: 0.585

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

GnomAD4 genome AF: 0.582 AC: 88490 AN: 151986 Hom.: 26640 Cov.: 32 AF XY: 0.584 AC XY: 43428 AN XY: 74306

Gnomad4 AFR AF: 0.738

Gnomad4 AMR AF: 0.593

Gnomad4 ASJ AF: 0.514

Gnomad4 EAS AF: 0.688

Gnomad4 SAS AF: 0.469

Gnomad4 FIN AF: 0.510

Gnomad4 NFE AF: 0.500

Gnomad4 OTH AF: 0.582

Alfa AF: 0.458 Hom.: 1929

Bravo AF: 0.600

Asia WGS AF: 0.576 AC: 2003 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	0.17
DANN	Benign	0.38

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4430531; hg19: chr11-134942626;