rs4130337

Variant names:

• chr3-106647236-A-G
• rs4130337
• ENST00000660862.1:n.1939-15363T>C

Variant summary

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

The ENST00000660862.1(LINC00882):​n.1939-15363T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.158 in 151,984 control chromosomes in the GnomAD database, including 2,107 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 0.16 (2107 hom., cov: 32)
• Consequence: LINC00882 ENST00000660862.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.111

Genes affected

LINC00882 (HGNC:48568): (long intergenic non-protein coding RNA 882)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.315 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
LINC00882	ENST00000660862.1	n.1939-15363T>C		intron_variant	Intron 8 of 9

Frequencies

GnomAD3 genomes AF: 0.158 AC: 24022 AN: 151866 Hom.: 2106 Cov.: 32

Gnomad AFR AF: 0.177

Gnomad AMI AF: 0.275

Gnomad AMR AF: 0.160

Gnomad ASJ AF: 0.184

Gnomad EAS AF: 0.329

Gnomad SAS AF: 0.240

Gnomad FIN AF: 0.0735

Gnomad MID AF: 0.152

Gnomad NFE AF: 0.137

Gnomad OTH AF: 0.174

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

GnomAD4 genome AF: 0.158 AC: 24034 AN: 151984 Hom.: 2107 Cov.: 32 AF XY: 0.156 AC XY: 11617 AN XY: 74298

Gnomad4 AFR AF: 0.177

Gnomad4 AMR AF: 0.160

Gnomad4 ASJ AF: 0.184

Gnomad4 EAS AF: 0.328

Gnomad4 SAS AF: 0.239

Gnomad4 FIN AF: 0.0735

Gnomad4 NFE AF: 0.138

Gnomad4 OTH AF: 0.175

Alfa AF: 0.145 Hom.: 433

Bravo AF: 0.168

Asia WGS AF: 0.271 AC: 938 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.9
DANN	Benign	0.58

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4130337; hg19: chr3-106366083;