11-25468936-G-T

Variant names:

• chr11-25468936-G-T
• rs10834691
• ENST00000812472.1:n.124+15274G>T

Variant summary

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

The ENST00000812472.1(ENSG00000305694):​n.124+15274G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.444 in 151,876 control chromosomes in the GnomAD database, including 18,002 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 (18002 hom., cov: 32)
• Consequence: ENSG00000305694 ENST00000812472.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.950
• Publications: 2 publications found

Genes affected

ENSG00000305694 (HGNC:):

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=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.845 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000812472.1. 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_183693.1		n.64-1569G>T		intron	N/A
	LINC02699	NR_183694.1		n.63+15274G>T		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000305694	ENST00000812472.1		n.124+15274G>T		intron	N/A
	ENSG00000305694	ENST00000812473.1		n.86-1569G>T		intron	N/A
	ENSG00000305694	ENST00000812474.1		n.65-1569G>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.444 AC: 67359 AN: 151758 Hom.: 17993 Cov.: 32

Gnomad AFR AF: 0.149

Gnomad AMI AF: 0.476

Gnomad AMR AF: 0.627

Gnomad ASJ AF: 0.555

Gnomad EAS AF: 0.867

Gnomad SAS AF: 0.544

Gnomad FIN AF: 0.514

Gnomad MID AF: 0.506

Gnomad NFE AF: 0.524

Gnomad OTH AF: 0.501

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

GnomAD4 genome AF: 0.444 AC: 67376 AN: 151876 Hom.: 18002 Cov.: 32 AF XY: 0.452 AC XY: 33553 AN XY: 74220

African (AFR) AF: 0.149 AC: 6163 AN: 41404

American (AMR) AF: 0.628 AC: 9584 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.555 AC: 1926 AN: 3470

East Asian (EAS) AF: 0.866 AC: 4470 AN: 5160

South Asian (SAS) AF: 0.544 AC: 2622 AN: 4820

European-Finnish (FIN) AF: 0.514 AC: 5410 AN: 10524

Middle Eastern (MID) AF: 0.483 AC: 141 AN: 292

European-Non Finnish (NFE) AF: 0.523 AC: 35562 AN: 67932

Other (OTH) AF: 0.505 AC: 1066 AN: 2110

Alfa AF: 0.334 Hom.: 4010

Bravo AF: 0.444

Asia WGS AF: 0.659 AC: 2282 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.42
DANN	Benign	0.14
PhyloP100		-0.95

Splicing

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

Other links and lift over

dbSNP: rs10834691; hg19: chr11-25490482;