11-25769312-C-G

Variant names:

• chr11-25769312-C-G
• rs1532289
• ENST00000526327.6:n.199-8382C>G

Variant summary

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

The ENST00000526327.6(LINC02699):​n.199-8382C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.175 in 151,370 control chromosomes in the GnomAD database, including 2,982 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 0.18 (2982 hom., cov: 30)
• Consequence: LINC02699 ENST00000526327.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0550
• Publications: 0 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 (NFE) allele frequency at 95% confidence interval = 0.245 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000526327.6. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02699	NR_183692.1		n.120-1159C>G		intron	N/A
	LINC02699	NR_183693.1		n.242-8382C>G		intron	N/A
	LINC02699	NR_183694.1		n.196-73283C>G		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02699	ENST00000526327.6	TSL:3	n.199-8382C>G		intron	N/A
	LINC02699	ENST00000533049.5	TSL:4	n.101-1159C>G		intron	N/A
	LINC02699	ENST00000533942.2	TSL:3	n.250-1159C>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.175 AC: 26537 AN: 151252 Hom.: 2980 Cov.: 30

Gnomad AFR AF: 0.0567

Gnomad AMI AF: 0.211

Gnomad AMR AF: 0.193

Gnomad ASJ AF: 0.302

Gnomad EAS AF: 0.00408

Gnomad SAS AF: 0.125

Gnomad FIN AF: 0.199

Gnomad MID AF: 0.297

Gnomad NFE AF: 0.248

Gnomad OTH AF: 0.215

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

GnomAD4 genome AF: 0.175 AC: 26527 AN: 151370 Hom.: 2982 Cov.: 30 AF XY: 0.173 AC XY: 12800 AN XY: 73942

African (AFR) AF: 0.0566 AC: 2341 AN: 41364

American (AMR) AF: 0.193 AC: 2915 AN: 15142

Ashkenazi Jewish (ASJ) AF: 0.302 AC: 1042 AN: 3454

East Asian (EAS) AF: 0.00409 AC: 21 AN: 5130

South Asian (SAS) AF: 0.125 AC: 601 AN: 4808

European-Finnish (FIN) AF: 0.199 AC: 2097 AN: 10514

Middle Eastern (MID) AF: 0.299 AC: 88 AN: 294

European-Non Finnish (NFE) AF: 0.248 AC: 16785 AN: 67652

Other (OTH) AF: 0.212 AC: 445 AN: 2100

Alfa AF: 0.118 Hom.: 236

Bravo AF: 0.171

Asia WGS AF: 0.0790 AC: 278 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.73
DANN	Benign	0.79
PhyloP100		-0.055

Splicing

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

Other links and lift over

dbSNP: rs1532289; hg19: chr11-25790859;