chr11-25793618-C-T

Variant names:

• chr11-25793618-C-T
• rs10219359
• NR_183694.1:n.196-48977C>T

Variant summary

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

The NR_183694.1(LINC02699):​n.196-48977C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.638 in 151,936 control chromosomes in the GnomAD database, including 31,841 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 0.64 (31841 hom., cov: 31)
• Consequence: LINC02699 NR_183694.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.921
• Publications: 2 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=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.714 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02699	NR_183694.1	n.196-48977C>T		intron_variant	Intron 2 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.638 AC: 96812 AN: 151818 Hom.: 31816 Cov.: 31

Gnomad AFR AF: 0.477

Gnomad AMI AF: 0.774

Gnomad AMR AF: 0.621

Gnomad ASJ AF: 0.563

Gnomad EAS AF: 0.734

Gnomad SAS AF: 0.731

Gnomad FIN AF: 0.712

Gnomad MID AF: 0.633

Gnomad NFE AF: 0.716

Gnomad OTH AF: 0.630

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

GnomAD4 genome AF: 0.638 AC: 96881 AN: 151936 Hom.: 31841 Cov.: 31 AF XY: 0.638 AC XY: 47377 AN XY: 74256

African (AFR) AF: 0.477 AC: 19754 AN: 41424

American (AMR) AF: 0.621 AC: 9479 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.563 AC: 1953 AN: 3466

East Asian (EAS) AF: 0.733 AC: 3785 AN: 5162

South Asian (SAS) AF: 0.731 AC: 3502 AN: 4790

European-Finnish (FIN) AF: 0.712 AC: 7513 AN: 10558

Middle Eastern (MID) AF: 0.639 AC: 188 AN: 294

European-Non Finnish (NFE) AF: 0.716 AC: 48663 AN: 67960

Other (OTH) AF: 0.635 AC: 1341 AN: 2112

Alfa AF: 0.683 Hom.: 61366

Bravo AF: 0.623

Asia WGS AF: 0.733 AC: 2549 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.3
DANN	Benign	0.60
PhyloP100		-0.92

Splicing

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

Other links and lift over

dbSNP: rs10219359; hg19: chr11-25815165;