11-25468936-G-T

Position:

• chr11-25468936-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_183694.1(LINC02699):​n.63+15274G>T variant causes a intron, non coding transcript 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: LINC02699 NR_183694.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.950

Genes affected

LINC02699 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC02699	NR_183694.1	n.63+15274G>T		intron_variant, non_coding_transcript_variant
LINC02699	NR_183693.1	n.64-1569G>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

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

Gnomad4 AFR AF: 0.149

Gnomad4 AMR AF: 0.628

Gnomad4 ASJ AF: 0.555

Gnomad4 EAS AF: 0.866

Gnomad4 SAS AF: 0.544

Gnomad4 FIN AF: 0.514

Gnomad4 NFE AF: 0.523

Gnomad4 OTH AF: 0.505

Alfa AF: 0.307 Hom.: 946

Bravo AF: 0.444

Asia WGS AF: 0.659 AC: 2282 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10834691; hg19: chr11-25490482;