rs780331

chr8-126048286-G-A

Variant summary

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

The ENST00000651482.1(LINC00861):n.366+60839C>T 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 0.597 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, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.23

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=-0.94).
• 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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC00861	ENST00000651482.1	n.366+60839C>T		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.336

Gnomad4 AMR AF: 0.732

Gnomad4 ASJ AF: 0.640

Gnomad4 EAS AF: 0.955

Gnomad4 SAS AF: 0.762

Gnomad4 FIN AF: 0.715

Gnomad4 NFE AF: 0.664

Gnomad4 OTH AF: 0.632

Alfa AF: 0.604 Hom.: 2736

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs780331; hg19: chr8-127060530;