8-126280186-C-T

Position:

• chr8-126280186-C-T

Variant summary

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

The ENST00000651482.1(LINC00861):​n.198+12405G>A variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.283 in 152,040 control chromosomes in the GnomAD database, including 6,121 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 0.28 (6121 hom., cov: 32)
• Consequence: LINC00861 ENST00000651482.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.248

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=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.304 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC00861	ENST00000651482.1	n.198+12405G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.283 AC: 42969 AN: 151920 Hom.: 6112 Cov.: 32

Gnomad AFR AF: 0.309

Gnomad AMI AF: 0.405

Gnomad AMR AF: 0.253

Gnomad ASJ AF: 0.235

Gnomad EAS AF: 0.300

Gnomad SAS AF: 0.303

Gnomad FIN AF: 0.274

Gnomad MID AF: 0.253

Gnomad NFE AF: 0.274

Gnomad OTH AF: 0.274

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

GnomAD4 genome AF: 0.283 AC: 42997 AN: 152040 Hom.: 6121 Cov.: 32 AF XY: 0.283 AC XY: 21031 AN XY: 74294

Gnomad4 AFR AF: 0.309

Gnomad4 AMR AF: 0.252

Gnomad4 ASJ AF: 0.235

Gnomad4 EAS AF: 0.300

Gnomad4 SAS AF: 0.303

Gnomad4 FIN AF: 0.274

Gnomad4 NFE AF: 0.273

Gnomad4 OTH AF: 0.278

Alfa AF: 0.263 Hom.: 881

Bravo AF: 0.278

Asia WGS AF: 0.308 AC: 1073 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	6.2
DANN	Benign	0.52

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13251380; hg19: chr8-127292431;