8-126071451-T-C

Variant names:

• chr8-126071451-T-C
• rs780321
• ENST00000651482.1:n.366+37674A>G

Variant summary

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

The ENST00000651482.1(LINC00861):​n.366+37674A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.645 in 152,014 control chromosomes in the GnomAD database, including 35,688 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 0.64 (35688 hom., cov: 31)
• Consequence: LINC00861 ENST00000651482.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0730
• Publications: 4 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 (EAS) allele frequency at 95% confidence interval = 0.947 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000651482.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC00861	ENST00000651482.1		n.366+37674A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.645 AC: 97966 AN: 151896 Hom.: 35680 Cov.: 31

Gnomad AFR AF: 0.276

Gnomad AMI AF: 0.734

Gnomad AMR AF: 0.795

Gnomad ASJ AF: 0.746

Gnomad EAS AF: 0.969

Gnomad SAS AF: 0.878

Gnomad FIN AF: 0.735

Gnomad MID AF: 0.816

Gnomad NFE AF: 0.771

Gnomad OTH AF: 0.716

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

GnomAD4 genome AF: 0.645 AC: 97979 AN: 152014 Hom.: 35688 Cov.: 31 AF XY: 0.653 AC XY: 48554 AN XY: 74302

African (AFR) AF: 0.276 AC: 11425 AN: 41442

American (AMR) AF: 0.796 AC: 12152 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.746 AC: 2590 AN: 3472

East Asian (EAS) AF: 0.969 AC: 5015 AN: 5174

South Asian (SAS) AF: 0.878 AC: 4234 AN: 4822

European-Finnish (FIN) AF: 0.735 AC: 7741 AN: 10534

Middle Eastern (MID) AF: 0.813 AC: 239 AN: 294

European-Non Finnish (NFE) AF: 0.771 AC: 52402 AN: 67984

Other (OTH) AF: 0.718 AC: 1513 AN: 2108

Alfa AF: 0.742 Hom.: 178722

Bravo AF: 0.632

Asia WGS AF: 0.873 AC: 3035 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.5
DANN	Benign	0.78
PhyloP100		-0.073

Splicing

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

Other links and lift over

dbSNP: rs780321; hg19: chr8-127083695;