1-229023085-C-T

Position:

• chr1-229023085-C-T

Variant summary

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

The ENST00000632635.1(LINC02815):​n.481-134G>A variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.695 in 152,190 control chromosomes in the GnomAD database, including 36,837 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 0.70 (36832 hom., cov: 33)
  • Exomes 𝑓: 0.70 (5 hom.)
• Consequence: LINC02815 ENST00000632635.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.36

Genes affected

LINC02815 (HGNC:54347): (long intergenic non-protein coding RNA 2815)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.761 is higher than 0.05.

Transcripts

RefSeq

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

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC02815	ENST00000632635.1	n.481-134G>A		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.695 AC: 105739 AN: 152052 Hom.: 36799 Cov.: 33

Gnomad AFR AF: 0.650

Gnomad AMI AF: 0.588

Gnomad AMR AF: 0.687

Gnomad ASJ AF: 0.731

Gnomad EAS AF: 0.675

Gnomad SAS AF: 0.782

Gnomad FIN AF: 0.771

Gnomad MID AF: 0.639

Gnomad NFE AF: 0.709

Gnomad OTH AF: 0.669

GnomAD4 exome AF: 0.700 AC: 14 AN: 20 Hom.: 5 AF XY: 0.688 AC XY: 11 AN XY: 16

Gnomad4 FIN exome AF: 0.833

Gnomad4 NFE exome AF: 0.600

Gnomad4 OTH exome AF: 0.750

GnomAD4 genome AF: 0.695 AC: 105811 AN: 152170 Hom.: 36832 Cov.: 33 AF XY: 0.701 AC XY: 52121 AN XY: 74392

Gnomad4 AFR AF: 0.649

Gnomad4 AMR AF: 0.688

Gnomad4 ASJ AF: 0.731

Gnomad4 EAS AF: 0.675

Gnomad4 SAS AF: 0.782

Gnomad4 FIN AF: 0.771

Gnomad4 NFE AF: 0.709

Gnomad4 OTH AF: 0.672

Alfa AF: 0.666 Hom.: 4720

Bravo AF: 0.685

Asia WGS AF: 0.721 AC: 2510 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	6.2
DANN	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs544528; hg19: chr1-229158832;