rs10956287

Variant names:

• chr8-126175138-G-A
• rs10956287
• ENST00000651482.1:n.199-62057C>T

Your query was ambiguous. Multiple possible variants found:

• 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 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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0890

Genes affected

LINC00861 (HGNC:45133): (long intergenic non-protein coding RNA 861)

RFPL4AP5 (HGNC:45144): (ret finger protein like 4A pseudogene 5)

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC00861	ENST00000651482.1	n.199-62057C>T		intron_variant	Intron 1 of 3
RFPL4AP5	ENST00000514977.1	n.-124C>T		upstream_gene_variant		6

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;