rs10834774

chr11-25737274-C-T

Variant summary

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

The NR_183694.1(LINC02699):n.196-105321C>T 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 0.755 in 151,696 control chromosomes in the GnomAD database, including 43,445 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 0.76 (43445 hom., cov: 32)
• Consequence: LINC02699 NR_183694.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.319

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=-0.9).
• 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.196-105321C>T		intron_variant, non_coding_transcript_variant
LINC02699	NR_183692.1	n.119+2405C>T		intron_variant, non_coding_transcript_variant
LINC02699	NR_183693.1	n.242-40420C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC02699	ENST00000526327.6	n.113+2405C>T		intron_variant, non_coding_transcript_variant		3
LINC02699	ENST00000533049.5	n.100+2405C>T		intron_variant, non_coding_transcript_variant		4
LINC02699	ENST00000533942.2	n.87+2405C>T		intron_variant, non_coding_transcript_variant		3
LINC02699	ENST00000654912.1	n.66+2405C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.755 AC: 114466 AN: 151578 Hom.: 43414 Cov.: 32

Gnomad AFR AF: 0.696

Gnomad AMI AF: 0.735

Gnomad AMR AF: 0.779

Gnomad ASJ AF: 0.853

Gnomad EAS AF: 0.676

Gnomad SAS AF: 0.684

Gnomad FIN AF: 0.740

Gnomad MID AF: 0.820

Gnomad NFE AF: 0.793

Gnomad OTH AF: 0.791

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

GnomAD4 genome AF: 0.755 AC: 114550 AN: 151696 Hom.: 43445 Cov.: 32 AF XY: 0.752 AC XY: 55762 AN XY: 74150

Gnomad4 AFR AF: 0.696

Gnomad4 AMR AF: 0.779

Gnomad4 ASJ AF: 0.853

Gnomad4 EAS AF: 0.676

Gnomad4 SAS AF: 0.685

Gnomad4 FIN AF: 0.740

Gnomad4 NFE AF: 0.793

Gnomad4 OTH AF: 0.787

Alfa AF: 0.770 Hom.: 7664

Bravo AF: 0.760

Asia WGS AF: 0.675 AC: 2349 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	1.5
Dann	Benign	0.57

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10834774; hg19: chr11-25758821;