rs1906493

Variant names:

• chr8-126080638-G-T
• rs1906493
• ENST00000651482.1:n.366+28487C>A

Variant summary

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

The ENST00000651482.1(LINC00861):​n.366+28487C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.132 in 152,122 control chromosomes in the GnomAD database, including 1,476 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 0.13 (1476 hom., cov: 32)
• Consequence: LINC00861 ENST00000651482.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0590

Genes affected

LINC00861 (HGNC:45133): (long intergenic non-protein coding RNA 861)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.202 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
LINC00861	ENST00000651482.1	n.366+28487C>A		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.132 AC: 20052 AN: 152004 Hom.: 1479 Cov.: 32

Gnomad AFR AF: 0.113

Gnomad AMI AF: 0.186

Gnomad AMR AF: 0.0892

Gnomad ASJ AF: 0.132

Gnomad EAS AF: 0.0628

Gnomad SAS AF: 0.214

Gnomad FIN AF: 0.166

Gnomad MID AF: 0.165

Gnomad NFE AF: 0.147

Gnomad OTH AF: 0.120

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

GnomAD4 genome AF: 0.132 AC: 20051 AN: 152122 Hom.: 1476 Cov.: 32 AF XY: 0.134 AC XY: 9946 AN XY: 74346

Gnomad4 AFR AF: 0.112

Gnomad4 AMR AF: 0.0890

Gnomad4 ASJ AF: 0.132

Gnomad4 EAS AF: 0.0630

Gnomad4 SAS AF: 0.213

Gnomad4 FIN AF: 0.166

Gnomad4 NFE AF: 0.147

Gnomad4 OTH AF: 0.120

Alfa AF: 0.142 Hom.: 1514

Bravo AF: 0.123

Asia WGS AF: 0.149 AC: 517 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.43
DANN	Benign	0.39

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1906493; hg19: chr8-127092882;