ENST00000526327.6:n.113+2405C>T

Variant names:

• chr11-25737274-C-T
• rs10834774
• ENST00000526327.6:n.113+2405C>T

Variant summary

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

The ENST00000526327.6(LINC02699):​n.113+2405C>T variant causes a intron 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 ENST00000526327.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.319
• Publications: 3 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=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.788 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02699	NR_183692.1		n.119+2405C>T		intron	N/A
	LINC02699	NR_183693.1		n.242-40420C>T		intron	N/A
	LINC02699	NR_183694.1		n.196-105321C>T		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02699	ENST00000526327.6	TSL:3	n.113+2405C>T		intron	N/A
	LINC02699	ENST00000533049.5	TSL:4	n.100+2405C>T		intron	N/A
	LINC02699	ENST00000533942.2	TSL:3	n.87+2405C>T		intron	N/A

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

African (AFR) AF: 0.696 AC: 28839 AN: 41436

American (AMR) AF: 0.779 AC: 11856 AN: 15212

Ashkenazi Jewish (ASJ) AF: 0.853 AC: 2951 AN: 3458

East Asian (EAS) AF: 0.676 AC: 3496 AN: 5168

South Asian (SAS) AF: 0.685 AC: 3299 AN: 4818

European-Finnish (FIN) AF: 0.740 AC: 7832 AN: 10580

Middle Eastern (MID) AF: 0.820 AC: 241 AN: 294

European-Non Finnish (NFE) AF: 0.793 AC: 53713 AN: 67718

Other (OTH) AF: 0.787 AC: 1656 AN: 2104

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.5
DANN	Benign	0.57
PhyloP100		-0.32

Splicing

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

Other links and lift over

dbSNP: rs10834774; hg19: chr11-25758821;