rs4482178

chr13-85529954-C-Achr13-85529954-C-T

Variant summary

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

The NR_046989.1(LINC00351):n.494-3122C>A 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 0.0848 in 151,772 control chromosomes in the GnomAD database, including 714 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 0.085 (714 hom., cov: 32)
• Consequence: LINC00351 NR_046989.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.10

Genes affected

LINC00351 (HGNC:42669): (long intergenic non-protein coding RNA 351)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.157 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC00351	NR_046989.1	n.494-3122C>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC00351	ENST00000424926.2	n.496-3122C>A		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.0849 AC: 12875 AN: 151654 Hom.: 715 Cov.: 32

Gnomad AFR AF: 0.0275

Gnomad AMI AF: 0.178

Gnomad AMR AF: 0.162

Gnomad ASJ AF: 0.0713

Gnomad EAS AF: 0.0757

Gnomad SAS AF: 0.0498

Gnomad FIN AF: 0.0650

Gnomad MID AF: 0.190

Gnomad NFE AF: 0.107

Gnomad OTH AF: 0.112

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

GnomAD4 genome AF: 0.0848 AC: 12872 AN: 151772 Hom.: 714 Cov.: 32 AF XY: 0.0839 AC XY: 6227 AN XY: 74180

Gnomad4 AFR AF: 0.0275

Gnomad4 AMR AF: 0.162

Gnomad4 ASJ AF: 0.0713

Gnomad4 EAS AF: 0.0753

Gnomad4 SAS AF: 0.0493

Gnomad4 FIN AF: 0.0650

Gnomad4 NFE AF: 0.107

Gnomad4 OTH AF: 0.112

Alfa AF: 0.108 Hom.: 813

Bravo AF: 0.0893

Asia WGS AF: 0.0510 AC: 177 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
Cadd	Benign	4.5
Dann	Benign	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4482178; hg19: chr13-86104089;