5-58184866-C-T

Variant names:

• chr5-58184866-C-T
• rs2964186
• ENST00000738711.1:n.186+12995G>A

Variant summary

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

The ENST00000738711.1(LINC02101):​n.186+12995G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.413 in 151,846 control chromosomes in the GnomAD database, including 13,601 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 0.41 (13601 hom., cov: 32)
• Consequence: LINC02101 ENST00000738711.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.942
• Publications: 2 publications found

Genes affected

LINC02101 (HGNC:52956): (long intergenic non-protein coding RNA 2101)

ENSG00000286853 (HGNC:):

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 (AFR) allele frequency at 95% confidence interval = 0.454 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
LINC02101	ENST00000738711.1	n.186+12995G>A		intron_variant	Intron 2 of 6
LINC02101	ENST00000738712.1	n.128+12995G>A		intron_variant	Intron 2 of 4
ENSG00000286853	ENST00000738819.1	n.141-9777C>T		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.413 AC: 62708 AN: 151728 Hom.: 13592 Cov.: 32

Gnomad AFR AF: 0.459

Gnomad AMI AF: 0.439

Gnomad AMR AF: 0.362

Gnomad ASJ AF: 0.381

Gnomad EAS AF: 0.0278

Gnomad SAS AF: 0.276

Gnomad FIN AF: 0.383

Gnomad MID AF: 0.380

Gnomad NFE AF: 0.442

Gnomad OTH AF: 0.411

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

GnomAD4 genome AF: 0.413 AC: 62743 AN: 151846 Hom.: 13601 Cov.: 32 AF XY: 0.404 AC XY: 29971 AN XY: 74218

African (AFR) AF: 0.459 AC: 19000 AN: 41392

American (AMR) AF: 0.361 AC: 5499 AN: 15232

Ashkenazi Jewish (ASJ) AF: 0.381 AC: 1317 AN: 3460

East Asian (EAS) AF: 0.0278 AC: 144 AN: 5172

South Asian (SAS) AF: 0.277 AC: 1334 AN: 4818

European-Finnish (FIN) AF: 0.383 AC: 4036 AN: 10542

Middle Eastern (MID) AF: 0.371 AC: 109 AN: 294

European-Non Finnish (NFE) AF: 0.442 AC: 30048 AN: 67922

Other (OTH) AF: 0.407 AC: 857 AN: 2106

Alfa AF: 0.436 Hom.: 1865

Bravo AF: 0.417

Asia WGS AF: 0.151 AC: 526 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.1
DANN	Benign	0.40
PhyloP100		-0.94

Splicing

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

Other links and lift over

dbSNP: rs2964186; hg19: chr5-57480693;