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. The variant received -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
• Publications: 1 publications found

Genes affected

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

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

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.500 AC: 1 AN: 2

Other (OTH) AC: 0 AN: 0

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

African (AFR) AF: 0.545 AC: 22572 AN: 41440

American (AMR) AF: 0.372 AC: 5675 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.250 AC: 869 AN: 3470

East Asian (EAS) AF: 0.357 AC: 1847 AN: 5172

South Asian (SAS) AF: 0.293 AC: 1410 AN: 4806

European-Finnish (FIN) AF: 0.322 AC: 3381 AN: 10502

Middle Eastern (MID) AF: 0.224 AC: 66 AN: 294

European-Non Finnish (NFE) AF: 0.286 AC: 19411 AN: 67974

Other (OTH) AF: 0.332 AC: 700 AN: 2110

Alfa AF: 0.323 Hom.: 2041

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
PhyloP100		-0.089

Splicing

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

Other links and lift over

dbSNP: rs10956287; hg19: chr8-127187382;