rs6484176

chr11-25766084-T-C

Variant summary

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

The NR_183694.1(LINC02699):n.196-76511T>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 0.3 in 151,760 control chromosomes in the GnomAD database, including 7,794 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 0.30 (7794 hom., cov: 32)
• Consequence: LINC02699 NR_183694.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0100

Genes affected

LINC02699 (HGNC:54213): (long intergenic non-protein coding RNA 2699)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.46 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC02699	NR_183694.1	n.196-76511T>C		intron_variant, non_coding_transcript_variant
LINC02699	NR_183692.1	n.120-4387T>C		intron_variant, non_coding_transcript_variant
LINC02699	NR_183693.1	n.242-11610T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC02699	ENST00000526327.6	n.199-11610T>C		intron_variant, non_coding_transcript_variant		3
LINC02699	ENST00000533049.5	n.101-4387T>C		intron_variant, non_coding_transcript_variant		4
LINC02699	ENST00000533942.2	n.173-1128T>C		intron_variant, non_coding_transcript_variant		3
LINC02699	ENST00000654912.1	n.191-4387T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.300 AC: 45483 AN: 151640 Hom.: 7784 Cov.: 32

Gnomad AFR AF: 0.465

Gnomad AMI AF: 0.209

Gnomad AMR AF: 0.240

Gnomad ASJ AF: 0.352

Gnomad EAS AF: 0.0758

Gnomad SAS AF: 0.186

Gnomad FIN AF: 0.198

Gnomad MID AF: 0.332

Gnomad NFE AF: 0.252

Gnomad OTH AF: 0.318

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

GnomAD4 genome AF: 0.300 AC: 45526 AN: 151760 Hom.: 7794 Cov.: 32 AF XY: 0.295 AC XY: 21916 AN XY: 74170

Gnomad4 AFR AF: 0.465

Gnomad4 AMR AF: 0.239

Gnomad4 ASJ AF: 0.352

Gnomad4 EAS AF: 0.0762

Gnomad4 SAS AF: 0.187

Gnomad4 FIN AF: 0.198

Gnomad4 NFE AF: 0.252

Gnomad4 OTH AF: 0.314

Alfa AF: 0.263 Hom.: 9192

Bravo AF: 0.312

Asia WGS AF: 0.163 AC: 569 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	9.4
Dann	Benign	0.83

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6484176; hg19: chr11-25787631;