rs10956287

Positions:

• chr8-126175138-G-A
• chr8-126175138-G-T

Variant summary

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

The ENST00000651482.1(LINC00861):​n.199-62057C>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 0.37 in 151,940 control chromosomes in the GnomAD database, including 11,385 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 0.37 (11385 hom., cov: 32)
  • Exomes 𝑓: 0.50 (0 hom.)
• Consequence: LINC00861 ENST00000651482.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0890

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=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.539 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.199-62057C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.370 AC: 56212 AN: 151820 Hom.: 11359 Cov.: 32

Gnomad AFR AF: 0.545

Gnomad AMI AF: 0.389

Gnomad AMR AF: 0.372

Gnomad ASJ AF: 0.250

Gnomad EAS AF: 0.357

Gnomad SAS AF: 0.294

Gnomad FIN AF: 0.322

Gnomad MID AF: 0.236

Gnomad NFE AF: 0.286

Gnomad OTH AF: 0.327

GnomAD4 exome AF: 0.500 AC: 1 AN: 2 Hom.: 0 AF XY: 0.500 AC XY: 1 AN XY: 2

Gnomad4 NFE exome AF: 0.500

GnomAD4 genome AF: 0.370 AC: 56286 AN: 151938 Hom.: 11385 Cov.: 32 AF XY: 0.370 AC XY: 27452 AN XY: 74208

Gnomad4 AFR AF: 0.545

Gnomad4 AMR AF: 0.372

Gnomad4 ASJ AF: 0.250

Gnomad4 EAS AF: 0.357

Gnomad4 SAS AF: 0.293

Gnomad4 FIN AF: 0.322

Gnomad4 NFE AF: 0.286

Gnomad4 OTH AF: 0.332

Alfa AF: 0.319 Hom.: 1938

Bravo AF: 0.384

Asia WGS AF: 0.354 AC: 1230 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	2.5
DANN	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10956287; hg19: chr8-127187382;