rs1532289

Variant names:

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

Your query was ambiguous. Multiple possible variants found:

• chr11-25769312-C-A
• chr11-25769312-C-G

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The ENST00000526327.6(LINC02699):​n.199-8382C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000132 in 151,418 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 0.000013 (0 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: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02699	NR_183692.1	n.120-1159C>A		intron_variant	Intron 1 of 4
LINC02699	NR_183693.1	n.242-8382C>A		intron_variant	Intron 3 of 5
LINC02699	NR_183694.1	n.196-73283C>A		intron_variant	Intron 2 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02699	ENST00000526327.6	n.199-8382C>A		intron_variant	Intron 2 of 4	3
LINC02699	ENST00000533049.5	n.101-1159C>A		intron_variant	Intron 1 of 4	4
LINC02699	ENST00000533942.2	n.250-1159C>A		intron_variant	Intron 3 of 4	3

Frequencies

GnomAD3 genomes AF: 0.0000132 AC: 2 AN: 151300 Hom.: 0 Cov.: 30

Gnomad AFR AF: 0.00

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000132

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00

Gnomad OTH AF: 0.00

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

GnomAD4 genome AF: 0.0000132 AC: 2 AN: 151418 Hom.: 0 Cov.: 30 AF XY: 0.0000135 AC XY: 1 AN XY: 73970

African (AFR) AF: 0.00 AC: 0 AN: 41372

American (AMR) AF: 0.000132 AC: 2 AN: 15152

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3454

East Asian (EAS) AF: 0.00 AC: 0 AN: 5130

South Asian (SAS) AF: 0.00 AC: 0 AN: 4810

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 10518

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 294

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 67672

Other (OTH) AF: 0.00 AC: 0 AN: 2104

Alfa AF: 0.00 Hom.: 236

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.71
DANN	Benign	0.78
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;