5-17362696-C-T

Variant names:

• chr5-17362696-C-T
• rs2036848
• ENST00000717181.1:n.523-2568G>A

Variant summary

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

The ENST00000717181.1(LINC02111):​n.523-2568G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.372 in 151,760 control chromosomes in the GnomAD database, including 10,697 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 0.37 (10697 hom., cov: 31)
• Consequence: LINC02111 ENST00000717181.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.35
• Publications: 0 publications found

Genes affected

LINC02111 (HGNC:52966): (long intergenic non-protein coding RNA 2111)

ENSG00000302913 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.474 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02111	ENST00000717181.1	n.523-2568G>A		intron_variant	Intron 5 of 5
ENSG00000302913	ENST00000790394.1	n.79-9229C>T		intron_variant	Intron 1 of 2
ENSG00000302913	ENST00000790395.1	n.74-17717C>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.373 AC: 56491 AN: 151642 Hom.: 10698 Cov.: 31

Gnomad AFR AF: 0.353

Gnomad AMI AF: 0.272

Gnomad AMR AF: 0.270

Gnomad ASJ AF: 0.365

Gnomad EAS AF: 0.405

Gnomad SAS AF: 0.492

Gnomad FIN AF: 0.421

Gnomad MID AF: 0.519

Gnomad NFE AF: 0.390

Gnomad OTH AF: 0.369

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

GnomAD4 genome AF: 0.372 AC: 56492 AN: 151760 Hom.: 10697 Cov.: 31 AF XY: 0.372 AC XY: 27606 AN XY: 74134

African (AFR) AF: 0.353 AC: 14587 AN: 41356

American (AMR) AF: 0.270 AC: 4116 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.365 AC: 1266 AN: 3466

East Asian (EAS) AF: 0.404 AC: 2082 AN: 5156

South Asian (SAS) AF: 0.490 AC: 2361 AN: 4818

European-Finnish (FIN) AF: 0.421 AC: 4412 AN: 10474

Middle Eastern (MID) AF: 0.517 AC: 151 AN: 292

European-Non Finnish (NFE) AF: 0.390 AC: 26496 AN: 67934

Other (OTH) AF: 0.367 AC: 775 AN: 2110

Alfa AF: 0.324 Hom.: 1580

Bravo AF: 0.358

Asia WGS AF: 0.423 AC: 1471 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.3
DANN	Benign	0.76
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs2036848; hg19: chr5-17362805; COSMIC: COSV59181217;