8-11762477-C-T

Position:

• chr8-11762477-C-T

Variant summary

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

The NR_171032.1(LINC02905):​n.1222C>T 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 0.25 in 191,220 control chromosomes in the GnomAD database, including 6,853 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 0.25 (5321 hom., cov: 31)
  • Exomes 𝑓: 0.25 (1532 hom.)
• Consequence: LINC02905 NR_171032.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.613

Genes affected

LINC02905 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.519 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC02905	NR_171032.1	n.1222C>T		non_coding_transcript_exon_variant	1/1
		n.11762477C>T		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.251 AC: 38121 AN: 151698 Hom.: 5320 Cov.: 31

Gnomad AFR AF: 0.321

Gnomad AMI AF: 0.129

Gnomad AMR AF: 0.232

Gnomad ASJ AF: 0.109

Gnomad EAS AF: 0.535

Gnomad SAS AF: 0.338

Gnomad FIN AF: 0.234

Gnomad MID AF: 0.237

Gnomad NFE AF: 0.198

Gnomad OTH AF: 0.228

GnomAD4 exome AF: 0.246 AC: 9674 AN: 39404 Hom.: 1532 Cov.: 0 AF XY: 0.249 AC XY: 5115 AN XY: 20570

Gnomad4 AFR exome AF: 0.331

Gnomad4 AMR exome AF: 0.241

Gnomad4 ASJ exome AF: 0.103

Gnomad4 EAS exome AF: 0.530

Gnomad4 SAS exome AF: 0.337

Gnomad4 FIN exome AF: 0.218

Gnomad4 NFE exome AF: 0.197

Gnomad4 OTH exome AF: 0.213

GnomAD4 genome AF: 0.251 AC: 38149 AN: 151816 Hom.: 5321 Cov.: 31 AF XY: 0.256 AC XY: 18989 AN XY: 74200

Gnomad4 AFR AF: 0.321

Gnomad4 AMR AF: 0.232

Gnomad4 ASJ AF: 0.109

Gnomad4 EAS AF: 0.536

Gnomad4 SAS AF: 0.337

Gnomad4 FIN AF: 0.234

Gnomad4 NFE AF: 0.198

Gnomad4 OTH AF: 0.229

Alfa AF: 0.156 Hom.: 463

Bravo AF: 0.252

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.7
DANN	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7015453; hg19: chr8-11619986;