rs780320

Variant names:

• chr8-126071258-T-A
• rs780320
• ENST00000651482.1:n.366+37867A>T

Your query was ambiguous. Multiple possible variants found:

• chr8-126071258-T-A
• chr8-126071258-T-C

Variant summary

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

The ENST00000651482.1(LINC00861):​n.366+37867A>T 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 152,126 control chromosomes in the GnomAD database, including 35,741 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 0.65 (35741 hom., cov: 33)
• Consequence: LINC00861 ENST00000651482.1 intron
• 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=-0.9).
• 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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC00861	ENST00000651482.1	n.366+37867A>T		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.646 AC: 98151 AN: 152008 Hom.: 35733 Cov.: 33

Gnomad AFR AF: 0.280

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: 0.820

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: 98170 AN: 152126 Hom.: 35741 Cov.: 33 AF XY: 0.654 AC XY: 48671 AN XY: 74384

Gnomad4 AFR AF: 0.279

Gnomad4 AMR AF: 0.795

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: 0.717

Alfa AF: 0.702 Hom.: 4799

Bravo AF: 0.633

Asia WGS AF: 0.876 AC: 3044 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	8.2
DANN	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs780320; hg19: chr8-127083502;