rs6484176

Variant names:

• chr11-25766084-T-C
• rs6484176
• ENST00000526327.6:n.199-11610T>C

Variant summary

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

The ENST00000526327.6(LINC02699):​n.199-11610T>C variant causes a intron 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 ENST00000526327.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0100
• Publications: 1 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
LINC02699	NR_183692.1	n.120-4387T>C		intron_variant	Intron 1 of 4
LINC02699	NR_183693.1	n.242-11610T>C		intron_variant	Intron 3 of 5
LINC02699	NR_183694.1	n.196-76511T>C		intron_variant	Intron 2 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02699	ENST00000526327.6	n.199-11610T>C		intron_variant	Intron 2 of 4	3
LINC02699	ENST00000533049.5	n.101-4387T>C		intron_variant	Intron 1 of 4	4
LINC02699	ENST00000533942.2	n.173-1128T>C		intron_variant	Intron 2 of 4	3

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

African (AFR) AF: 0.465 AC: 19264 AN: 41414

American (AMR) AF: 0.239 AC: 3642 AN: 15212

Ashkenazi Jewish (ASJ) AF: 0.352 AC: 1218 AN: 3460

East Asian (EAS) AF: 0.0762 AC: 393 AN: 5158

South Asian (SAS) AF: 0.187 AC: 900 AN: 4822

European-Finnish (FIN) AF: 0.198 AC: 2099 AN: 10590

Middle Eastern (MID) AF: 0.337 AC: 99 AN: 294

European-Non Finnish (NFE) AF: 0.252 AC: 17060 AN: 67794

Other (OTH) AF: 0.314 AC: 661 AN: 2106

Alfa AF: 0.268 Hom.: 22388

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
PhyloP100		0.010

Splicing

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

Other links and lift over

dbSNP: rs6484176; hg19: chr11-25787631;