rs236212

chr10-118359086-T-C

Variant summary

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

The NR_108045.1(LINC00867):n.463T>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.196 in 152,258 control chromosomes in the GnomAD database, including 3,140 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 0.20 (3140 hom., cov: 32)
  • Exomes 𝑓: 0.50 (0 hom.)
• Consequence: LINC00867 NR_108045.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.727

Genes affected

LINC00867 (HGNC:45265): (long intergenic non-protein coding RNA 867)

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 (AMR) allele frequency at 95% confidence interval = 0.257 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC00867	NR_108045.1	n.463T>C		non_coding_transcript_exon_variant	3/3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC00867	ENST00000668223.1	n.469+1238T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.196 AC: 29783 AN: 152138 Hom.: 3139 Cov.: 32

Gnomad AFR AF: 0.105

Gnomad AMI AF: 0.182

Gnomad AMR AF: 0.263

Gnomad ASJ AF: 0.174

Gnomad EAS AF: 0.250

Gnomad SAS AF: 0.186

Gnomad FIN AF: 0.169

Gnomad MID AF: 0.168

Gnomad NFE AF: 0.238

Gnomad OTH AF: 0.202

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

Gnomad4 NFE exome AF: 0.500

GnomAD4 genome AF: 0.196 AC: 29791 AN: 152256 Hom.: 3140 Cov.: 32 AF XY: 0.196 AC XY: 14573 AN XY: 74438

Gnomad4 AFR AF: 0.105

Gnomad4 AMR AF: 0.264

Gnomad4 ASJ AF: 0.174

Gnomad4 EAS AF: 0.251

Gnomad4 SAS AF: 0.186

Gnomad4 FIN AF: 0.169

Gnomad4 NFE AF: 0.238

Gnomad4 OTH AF: 0.204

Alfa AF: 0.230 Hom.: 8662

Bravo AF: 0.202

Asia WGS AF: 0.202 AC: 705 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	8.7
Dann	Benign	0.58

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs236212; hg19: chr10-120118598;