chr8-126048286-G-A

Variant names:

• chr8-126048286-G-A
• rs780331
• ENST00000651482.1:n.366+60839C>T

Variant summary

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

The ENST00000651482.1(LINC00861):​n.366+60839C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.597 in 152,034 control chromosomes in the GnomAD database, including 29,355 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 0.60 (29355 hom., cov: 32)
• Consequence: LINC00861 ENST00000651482.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.23
• Publications: 2 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=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.933 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+60839C>T		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.597 AC: 90676 AN: 151916 Hom.: 29343 Cov.: 32

Gnomad AFR AF: 0.337

Gnomad AMI AF: 0.605

Gnomad AMR AF: 0.731

Gnomad ASJ AF: 0.640

Gnomad EAS AF: 0.955

Gnomad SAS AF: 0.761

Gnomad FIN AF: 0.715

Gnomad MID AF: 0.661

Gnomad NFE AF: 0.664

Gnomad OTH AF: 0.632

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

GnomAD4 genome AF: 0.597 AC: 90710 AN: 152034 Hom.: 29355 Cov.: 32 AF XY: 0.609 AC XY: 45230 AN XY: 74320

African (AFR) AF: 0.336 AC: 13941 AN: 41452

American (AMR) AF: 0.732 AC: 11183 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.640 AC: 2218 AN: 3464

East Asian (EAS) AF: 0.955 AC: 4940 AN: 5174

South Asian (SAS) AF: 0.762 AC: 3667 AN: 4812

European-Finnish (FIN) AF: 0.715 AC: 7558 AN: 10574

Middle Eastern (MID) AF: 0.660 AC: 194 AN: 294

European-Non Finnish (NFE) AF: 0.664 AC: 45123 AN: 67960

Other (OTH) AF: 0.632 AC: 1335 AN: 2112

Alfa AF: 0.635 Hom.: 11219

Bravo AF: 0.585

Asia WGS AF: 0.799 AC: 2776 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.28
DANN	Benign	0.44
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs780331; hg19: chr8-127060530;