ENST00000507817.3:n.271+60572C>T

Variant names:

• chr4-187605190-G-A
• rs13147499
• ENST00000507817.3:n.271+60572C>T

Variant summary

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

The ENST00000507817.3(LINC02492):​n.271+60572C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.331 in 151,906 control chromosomes in the GnomAD database, including 8,703 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 0.33 (8703 hom., cov: 32)
• Consequence: LINC02492 ENST00000507817.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.16
• Publications: 2 publications found

Genes affected

LINC02492 (HGNC:53476): (long intergenic non-protein coding RNA 2492)

LOC105377604 (HGNC:):

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 = 0.452 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02492	NR_110436.1	n.157+60572C>T		intron_variant	Intron 2 of 2
LOC105377604	XR_939612.3	n.156-12263C>T		intron_variant	Intron 1 of 3
LOC105377604	XR_939613.3	n.156-12263C>T		intron_variant	Intron 1 of 3
LOC105377604	XR_939614.3	n.156-12263C>T		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02492	ENST00000507817.3	n.271+60572C>T		intron_variant	Intron 2 of 2	2
LINC02492	ENST00000514767.2	n.161+41020C>T		intron_variant	Intron 1 of 3	3
LINC02492	ENST00000515660.6	n.159-22660C>T		intron_variant	Intron 1 of 5	2

Frequencies

GnomAD3 genomes AF: 0.331 AC: 50212 AN: 151788 Hom.: 8709 Cov.: 32

Gnomad AFR AF: 0.230

Gnomad AMI AF: 0.458

Gnomad AMR AF: 0.288

Gnomad ASJ AF: 0.438

Gnomad EAS AF: 0.468

Gnomad SAS AF: 0.360

Gnomad FIN AF: 0.283

Gnomad MID AF: 0.471

Gnomad NFE AF: 0.388

Gnomad OTH AF: 0.347

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

GnomAD4 genome AF: 0.331 AC: 50207 AN: 151906 Hom.: 8703 Cov.: 32 AF XY: 0.325 AC XY: 24120 AN XY: 74234

African (AFR) AF: 0.230 AC: 9542 AN: 41414

American (AMR) AF: 0.287 AC: 4383 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.438 AC: 1517 AN: 3466

East Asian (EAS) AF: 0.467 AC: 2399 AN: 5134

South Asian (SAS) AF: 0.359 AC: 1730 AN: 4814

European-Finnish (FIN) AF: 0.283 AC: 2980 AN: 10544

Middle Eastern (MID) AF: 0.469 AC: 137 AN: 292

European-Non Finnish (NFE) AF: 0.388 AC: 26377 AN: 67952

Other (OTH) AF: 0.344 AC: 725 AN: 2108

Alfa AF: 0.380 Hom.: 12761

Bravo AF: 0.327

Asia WGS AF: 0.384 AC: 1336 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	0.17
DANN	Benign	0.60
PhyloP100		-2.2

Splicing

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

Other links and lift over

dbSNP: rs13147499; hg19: chr4-188526344;