rs11028909

chr11-25750898-G-Achr11-25750898-G-C

Variant summary

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

The NR_183694.1(LINC02699):n.196-91697G>A 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 0.754 in 151,942 control chromosomes in the GnomAD database, including 43,372 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 0.75 (43372 hom., cov: 31)
• Consequence: LINC02699 NR_183694.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.387

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 (NFE) allele frequency at 95% confidence interval = 0.788 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC02699	NR_183694.1	n.196-91697G>A		intron_variant, non_coding_transcript_variant
LINC02699	NR_183692.1	n.119+16029G>A		intron_variant, non_coding_transcript_variant
LINC02699	NR_183693.1	n.242-26796G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC02699	ENST00000526327.6	n.198+10338G>A		intron_variant, non_coding_transcript_variant		3
LINC02699	ENST00000533049.5	n.100+16029G>A		intron_variant, non_coding_transcript_variant		4
LINC02699	ENST00000533942.2	n.172+10338G>A		intron_variant, non_coding_transcript_variant		3
LINC02699	ENST00000654912.1	n.190+7799G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.754 AC: 114466 AN: 151824 Hom.: 43352 Cov.: 31

Gnomad AFR AF: 0.691

Gnomad AMI AF: 0.734

Gnomad AMR AF: 0.778

Gnomad ASJ AF: 0.853

Gnomad EAS AF: 0.676

Gnomad SAS AF: 0.685

Gnomad FIN AF: 0.741

Gnomad MID AF: 0.820

Gnomad NFE AF: 0.793

Gnomad OTH AF: 0.789

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

GnomAD4 genome AF: 0.754 AC: 114532 AN: 151942 Hom.: 43372 Cov.: 31 AF XY: 0.751 AC XY: 55747 AN XY: 74278

Gnomad4 AFR AF: 0.691

Gnomad4 AMR AF: 0.778

Gnomad4 ASJ AF: 0.853

Gnomad4 EAS AF: 0.677

Gnomad4 SAS AF: 0.686

Gnomad4 FIN AF: 0.741

Gnomad4 NFE AF: 0.793

Gnomad4 OTH AF: 0.785

Alfa AF: 0.769 Hom.: 7646

Bravo AF: 0.759

Asia WGS AF: 0.668 AC: 2314 AN: 3460

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	3.7
Dann	Benign	0.58

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11028909; hg19: chr11-25772445;