11-116655150-C-T

Variant names:

• chr11-116655150-C-T
• rs481843
• ENST00000439483.3:n.385C>T

Variant summary

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

The ENST00000439483.3(LINC02702):​n.385C>T 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 0.0884 in 152,256 control chromosomes in the GnomAD database, including 687 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 0.088 (687 hom., cov: 32)
  • Exomes 𝑓: 0.056 (0 hom.)
• Consequence: LINC02702 ENST00000439483.3 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.07
• Publications: 15 publications found

Genes affected

LINC02702 (HGNC:54217): (long intergenic non-protein coding RNA 2702)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.109 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02702	NR_135069.1	n.272+2097C>T		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02702	ENST00000439483.3	n.385C>T		non_coding_transcript_exon_variant	Exon 3 of 4	2
LINC02702	ENST00000669244.1	n.670C>T		non_coding_transcript_exon_variant	Exon 3 of 4
LINC02702	ENST00000444123.6	n.272+2097C>T		intron_variant	Intron 2 of 2	5
LINC02702	ENST00000665087.1	n.508+1775C>T		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.0883 AC: 13438 AN: 152102 Hom.: 686 Cov.: 32

Gnomad AFR AF: 0.0644

Gnomad AMI AF: 0.0570

Gnomad AMR AF: 0.105

Gnomad ASJ AF: 0.0988

Gnomad EAS AF: 0.106

Gnomad SAS AF: 0.116

Gnomad FIN AF: 0.181

Gnomad MID AF: 0.104

Gnomad NFE AF: 0.0815

Gnomad OTH AF: 0.0842

GnomAD4 exome AF: 0.0556 AC: 2 AN: 36 Hom.: 0 Cov.: 0 AF XY: 0.0455 AC XY: 1 AN XY: 22

African (AFR) AF: 0.00 AC: 0 AN: 2

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.0909 AC: 2 AN: 22

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 12

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.0884 AC: 13451 AN: 152220 Hom.: 687 Cov.: 32 AF XY: 0.0938 AC XY: 6978 AN XY: 74426

African (AFR) AF: 0.0644 AC: 2677 AN: 41558

American (AMR) AF: 0.105 AC: 1603 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.0988 AC: 343 AN: 3472

East Asian (EAS) AF: 0.106 AC: 549 AN: 5178

South Asian (SAS) AF: 0.117 AC: 562 AN: 4824

European-Finnish (FIN) AF: 0.181 AC: 1914 AN: 10570

Middle Eastern (MID) AF: 0.109 AC: 32 AN: 294

European-Non Finnish (NFE) AF: 0.0815 AC: 5541 AN: 68002

Other (OTH) AF: 0.0843 AC: 178 AN: 2112

Alfa AF: 0.0822 Hom.: 918

Bravo AF: 0.0842

Asia WGS AF: 0.107 AC: 371 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.5
DANN	Benign	0.71
PhyloP100		-1.1
Mutation Taster		=99/1	polymorphism

Splicing

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

Other links and lift over

dbSNP: rs481843; hg19: chr11-116525867;