rs1906493

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 7 publications found

Genes affected

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

ENSG00000302796 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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
ENSG00000302796	ENST00000789606.1	n.398+3047C>A		intron_variant	Intron 4 of 5

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

African (AFR) AF: 0.112 AC: 4663 AN: 41504

American (AMR) AF: 0.0890 AC: 1360 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.132 AC: 457 AN: 3468

East Asian (EAS) AF: 0.0630 AC: 326 AN: 5178

South Asian (SAS) AF: 0.213 AC: 1028 AN: 4820

European-Finnish (FIN) AF: 0.166 AC: 1755 AN: 10558

Middle Eastern (MID) AF: 0.160 AC: 47 AN: 294

European-Non Finnish (NFE) AF: 0.147 AC: 9991 AN: 68000

Other (OTH) AF: 0.120 AC: 254 AN: 2112

Alfa AF: 0.138 Hom.: 2598

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
PhyloP100		0.059

Splicing

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

Other links and lift over

dbSNP: rs1906493; hg19: chr8-127092882;