chr11-25769598-G-T

Variant names:

• chr11-25769598-G-T
• rs1389421
• ENST00000526327.6:n.199-8096G>T

Variant summary

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

The ENST00000526327.6(LINC02699):​n.199-8096G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.44 in 150,658 control chromosomes in the GnomAD database, including 15,994 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 0.44 (15994 hom., cov: 28)
• Consequence: LINC02699 ENST00000526327.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.565
• 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=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.601 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.120-873G>T		intron	N/A
	LINC02699	NR_183693.1		n.242-8096G>T		intron	N/A
	LINC02699	NR_183694.1		n.196-72997G>T		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02699	ENST00000526327.6	TSL:3	n.199-8096G>T		intron	N/A
	LINC02699	ENST00000533049.5	TSL:4	n.101-873G>T		intron	N/A
	LINC02699	ENST00000533942.2	TSL:3	n.250-873G>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.440 AC: 66230 AN: 150542 Hom.: 15986 Cov.: 28

Gnomad AFR AF: 0.220

Gnomad AMI AF: 0.523

Gnomad AMR AF: 0.516

Gnomad ASJ AF: 0.468

Gnomad EAS AF: 0.619

Gnomad SAS AF: 0.508

Gnomad FIN AF: 0.517

Gnomad MID AF: 0.491

Gnomad NFE AF: 0.523

Gnomad OTH AF: 0.457

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

GnomAD4 genome AF: 0.440 AC: 66259 AN: 150658 Hom.: 15994 Cov.: 28 AF XY: 0.440 AC XY: 32356 AN XY: 73464

African (AFR) AF: 0.220 AC: 9078 AN: 41234

American (AMR) AF: 0.517 AC: 7760 AN: 15024

Ashkenazi Jewish (ASJ) AF: 0.468 AC: 1609 AN: 3440

East Asian (EAS) AF: 0.619 AC: 3112 AN: 5030

South Asian (SAS) AF: 0.509 AC: 2439 AN: 4796

European-Finnish (FIN) AF: 0.517 AC: 5354 AN: 10358

Middle Eastern (MID) AF: 0.486 AC: 143 AN: 294

European-Non Finnish (NFE) AF: 0.524 AC: 35336 AN: 67492

Other (OTH) AF: 0.458 AC: 954 AN: 2084

Alfa AF: 0.454 Hom.: 2879

Bravo AF: 0.434

Asia WGS AF: 0.517 AC: 1796 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	7.9
DANN	Benign	0.69
PhyloP100		0.56

Splicing

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

Other links and lift over

dbSNP: rs1389421; hg19: chr11-25791145;