rs780321

Positions:

• chr8-126071451-T-C
• chr8-126071451-T-G

Variant summary

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

The ENST00000651482.1(LINC00861):​n.366+37674A>G 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 0.645 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, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0730

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=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.947 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC00861	ENST00000651482.1	n.366+37674A>G		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.276

Gnomad4 AMR AF: 0.796

Gnomad4 ASJ AF: 0.746

Gnomad4 EAS AF: 0.969

Gnomad4 SAS AF: 0.878

Gnomad4 FIN AF: 0.735

Gnomad4 NFE AF: 0.771

Gnomad4 OTH AF: 0.718

Alfa AF: 0.763 Hom.: 88284

Bravo AF: 0.632

Asia WGS AF: 0.873 AC: 3035 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs780321; hg19: chr8-127083695;