rs13147499

Positions:

• chr4-187605190-G-A
• chr4-187605190-G-T

Variant summary

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

The NR_110436.1(LINC02492):​n.157+60572C>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 0.331 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 NR_110436.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.16

Genes affected

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

LOC105377604 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
LINC02492	NR_110436.1	n.157+60572C>T		intron_variant, non_coding_transcript_variant
LOC105377604	XR_939614.3	n.156-12263C>T		intron_variant, non_coding_transcript_variant
LOC105377604	XR_939612.3	n.156-12263C>T		intron_variant, non_coding_transcript_variant
LOC105377604	XR_939613.3	n.156-12263C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC02492	ENST00000507817.2	n.271+60572C>T		intron_variant, non_coding_transcript_variant		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

Gnomad4 AFR AF: 0.230

Gnomad4 AMR AF: 0.287

Gnomad4 ASJ AF: 0.438

Gnomad4 EAS AF: 0.467

Gnomad4 SAS AF: 0.359

Gnomad4 FIN AF: 0.283

Gnomad4 NFE AF: 0.388

Gnomad4 OTH AF: 0.344

Alfa AF: 0.379 Hom.: 11100

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13147499; hg19: chr4-188526344;