8-126230030-C-T

Variant names:

• chr8-126230030-C-T
• rs6470418
• ENST00000651482.1:n.198+62561G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000651482.1(LINC00861):​n.198+62561G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.356 in 151,926 control chromosomes in the GnomAD database, including 10,225 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 0.36 (10225 hom., cov: 32)
• Consequence: LINC00861 ENST00000651482.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.832
• Publications: 1 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.488 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.198+62561G>A		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.355 AC: 53949 AN: 151808 Hom.: 10205 Cov.: 32

Gnomad AFR AF: 0.494

Gnomad AMI AF: 0.403

Gnomad AMR AF: 0.370

Gnomad ASJ AF: 0.229

Gnomad EAS AF: 0.357

Gnomad SAS AF: 0.295

Gnomad FIN AF: 0.323

Gnomad MID AF: 0.201

Gnomad NFE AF: 0.284

Gnomad OTH AF: 0.330

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

GnomAD4 genome AF: 0.356 AC: 54022 AN: 151926 Hom.: 10225 Cov.: 32 AF XY: 0.356 AC XY: 26392 AN XY: 74236

African (AFR) AF: 0.494 AC: 20456 AN: 41410

American (AMR) AF: 0.371 AC: 5657 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.229 AC: 793 AN: 3468

East Asian (EAS) AF: 0.357 AC: 1842 AN: 5158

South Asian (SAS) AF: 0.294 AC: 1419 AN: 4820

European-Finnish (FIN) AF: 0.323 AC: 3407 AN: 10542

Middle Eastern (MID) AF: 0.188 AC: 55 AN: 292

European-Non Finnish (NFE) AF: 0.284 AC: 19320 AN: 67946

Other (OTH) AF: 0.334 AC: 706 AN: 2112

Alfa AF: 0.234 Hom.: 799

Bravo AF: 0.367

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.65
DANN	Benign	0.52
PhyloP100		-0.83

Splicing

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

Other links and lift over

dbSNP: rs6470418; hg19: chr8-127242274;