rs4871297

chr8-122693916-G-Achr8-122693916-G-Cchr8-122693916-G-T

Variant summary

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

The NR_126348.1(LINC01151):n.191C>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 0.546 in 152,144 control chromosomes in the GnomAD database, including 22,816 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 0.55 (22816 hom., cov: 33)
  • Exomes 𝑓: 0.25 (0 hom.)
• Consequence: LINC01151 NR_126348.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.198

Genes affected

LINC01151 (HGNC:49471): (long intergenic non-protein coding RNA 1151)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.68).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.618 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC01151	NR_126348.1	n.191C>T		non_coding_transcript_exon_variant	1/4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC01151	ENST00000664854.1	n.175C>T		non_coding_transcript_exon_variant	1/4

Frequencies

GnomAD3 genomes AF: 0.546 AC: 82963 AN: 152022 Hom.: 22800 Cov.: 33

Gnomad AFR AF: 0.587

Gnomad AMI AF: 0.374

Gnomad AMR AF: 0.445

Gnomad ASJ AF: 0.588

Gnomad EAS AF: 0.637

Gnomad SAS AF: 0.575

Gnomad FIN AF: 0.521

Gnomad MID AF: 0.557

Gnomad NFE AF: 0.539

Gnomad OTH AF: 0.532

GnomAD4 exome AF: 0.250 AC: 1 AN: 4 Hom.: 0 Cov.: 0 AF XY: 0.500 AC XY: 1 AN XY: 2

Gnomad4 FIN exome AF: 0.250

GnomAD4 genome AF: 0.546 AC: 83006 AN: 152140 Hom.: 22816 Cov.: 33 AF XY: 0.543 AC XY: 40400 AN XY: 74390

Gnomad4 AFR AF: 0.587

Gnomad4 AMR AF: 0.444

Gnomad4 ASJ AF: 0.588

Gnomad4 EAS AF: 0.636

Gnomad4 SAS AF: 0.576

Gnomad4 FIN AF: 0.521

Gnomad4 NFE AF: 0.539

Gnomad4 OTH AF: 0.527

Alfa AF: 0.538 Hom.: 12502

Bravo AF: 0.535

Asia WGS AF: 0.596 AC: 2075 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.68
Cadd	Benign	8.5
Dann	Benign	0.82

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4871297; hg19: chr8-123706155;