3-25872392-A-G

Variant summary

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

The NR_034055.1(LINC00692):n.146T>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 0.665 in 152,128 control chromosomes in the GnomAD database, including 38,475 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 0.67 (38465 hom., cov: 33)
  • Exomes 𝑓: 0.92 (10 hom.)
• Consequence: LINC00692 NR_034055.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.12

Genes affected

LINC00692 (HGNC:27708): (long intergenic non-protein coding RNA 692)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.939 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC00692	NR_034055.1	n.146T>C		non_coding_transcript_exon_variant	2/8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC00692	ENST00000451284.6	n.199T>C		non_coding_transcript_exon_variant	2/8	1
LINC00692	ENST00000655652.1	n.156T>C		non_coding_transcript_exon_variant	2/8
LINC00692	ENST00000496997.1	n.115T>C		non_coding_transcript_exon_variant	2/5	5

Frequencies

GnomAD3 genomes AF: 0.666 AC: 101163 AN: 151986 Hom.: 38450 Cov.: 33

Gnomad AFR AF: 0.267

Gnomad AMI AF: 0.770

Gnomad AMR AF: 0.799

Gnomad ASJ AF: 0.843

Gnomad EAS AF: 0.961

Gnomad SAS AF: 0.741

Gnomad FIN AF: 0.815

Gnomad MID AF: 0.861

Gnomad NFE AF: 0.814

Gnomad OTH AF: 0.713

GnomAD4 exome AF: 0.917 AC: 22 AN: 24 Hom.: 10 Cov.: 0 AF XY: 0.950 AC XY: 19 AN XY: 20

Gnomad4 AFR exome AF: 1.00

Gnomad4 FIN exome AF: 0.500

Gnomad4 NFE exome AF: 0.944

GnomAD4 genome AF: 0.665 AC: 101206 AN: 152104 Hom.: 38465 Cov.: 33 AF XY: 0.672 AC XY: 49979 AN XY: 74368

Gnomad4 AFR AF: 0.267

Gnomad4 AMR AF: 0.799

Gnomad4 ASJ AF: 0.843

Gnomad4 EAS AF: 0.961

Gnomad4 SAS AF: 0.743

Gnomad4 FIN AF: 0.815

Gnomad4 NFE AF: 0.814

Gnomad4 OTH AF: 0.716

Alfa AF: 0.798 Hom.: 80517

Bravo AF: 0.648

Asia WGS AF: 0.760 AC: 2641 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
Cadd	Benign	0.51
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: rs6551000; hg19: chr3-25913883;