11-25750898-G-A

Variant names:

• chr11-25750898-G-A
• rs11028909
• ENST00000526327.6:n.198+10338G>A

Variant summary

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

The ENST00000526327.6(LINC02699):​n.198+10338G>A variant causes a intron 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 ENST00000526327.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.387
• Publications: 4 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=-0.91).
• 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02699	NR_183692.1		n.119+16029G>A		intron	N/A
	LINC02699	NR_183693.1		n.242-26796G>A		intron	N/A
	LINC02699	NR_183694.1		n.196-91697G>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02699	ENST00000526327.6	TSL:3	n.198+10338G>A		intron	N/A
	LINC02699	ENST00000533049.5	TSL:4	n.100+16029G>A		intron	N/A
	LINC02699	ENST00000533942.2	TSL:3	n.172+10338G>A		intron	N/A

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

African (AFR) AF: 0.691 AC: 28628 AN: 41430

American (AMR) AF: 0.778 AC: 11879 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.853 AC: 2960 AN: 3470

East Asian (EAS) AF: 0.677 AC: 3491 AN: 5158

South Asian (SAS) AF: 0.686 AC: 3308 AN: 4824

European-Finnish (FIN) AF: 0.741 AC: 7805 AN: 10540

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

European-Non Finnish (NFE) AF: 0.793 AC: 53891 AN: 67936

Other (OTH) AF: 0.785 AC: 1660 AN: 2114

Alfa AF: 0.766 Hom.: 7818

Bravo AF: 0.759

Asia WGS AF: 0.668 AC: 2314 AN: 3460

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.7
DANN	Benign	0.58
PhyloP100		0.39

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs11028909;

hg19: chr11-25772445;