rs1517605

Variant names:

• chr3-106905447-T-C
• rs1517605
• ENST00000484698.5:n.628+15519A>G

Variant summary

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

The ENST00000484698.5(LINC00882):​n.628+15519A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.138 in 152,134 control chromosomes in the GnomAD database, including 1,625 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 0.14 (1625 hom., cov: 32)
• Consequence: LINC00882 ENST00000484698.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.209

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=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.166 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	ENST00000484698.5	n.628+15519A>G		intron_variant	Intron 6 of 7	1
LINC00882	ENST00000655451.1	n.729+7595A>G		intron_variant	Intron 7 of 8
LINC00882	ENST00000656342.1	n.965+15519A>G		intron_variant	Intron 7 of 8

Frequencies

GnomAD3 genomes AF: 0.139 AC: 21055 AN: 152014 Hom.: 1623 Cov.: 32

Gnomad AFR AF: 0.169

Gnomad AMI AF: 0.0121

Gnomad AMR AF: 0.0973

Gnomad ASJ AF: 0.151

Gnomad EAS AF: 0.000965

Gnomad SAS AF: 0.0439

Gnomad FIN AF: 0.184

Gnomad MID AF: 0.0955

Gnomad NFE AF: 0.140

Gnomad OTH AF: 0.133

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

GnomAD4 genome AF: 0.138 AC: 21063 AN: 152134 Hom.: 1625 Cov.: 32 AF XY: 0.137 AC XY: 10158 AN XY: 74386

Gnomad4 AFR AF: 0.169

Gnomad4 AMR AF: 0.0971

Gnomad4 ASJ AF: 0.151

Gnomad4 EAS AF: 0.000967

Gnomad4 SAS AF: 0.0447

Gnomad4 FIN AF: 0.184

Gnomad4 NFE AF: 0.140

Gnomad4 OTH AF: 0.131

Alfa AF: 0.136 Hom.: 2117

Bravo AF: 0.135

Asia WGS AF: 0.0300 AC: 104 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.1
DANN	Benign	0.57

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1517605; hg19: chr3-106624294;