rs1017920

chr2-8419050-G-A

Variant summary

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

The ENST00000655671.1(LINC00299):n.49-26082C>T 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 0.0712 in 152,236 control chromosomes in the GnomAD database, including 594 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 0.071 (594 hom., cov: 31)
• Consequence: LINC00299 ENST00000655671.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.695

Genes affected

LINC00299 (HGNC:27940): (long intergenic non-protein coding RNA 299)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.263 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC00299	ENST00000655671.1	n.49-26082C>T		intron_variant, non_coding_transcript_variant
LINC00299	ENST00000661371.1	n.90-26082C>T		intron_variant, non_coding_transcript_variant
LINC00299	ENST00000669954.1	n.175+2404C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0712 AC: 10824 AN: 152118 Hom.: 592 Cov.: 31

Gnomad AFR AF: 0.0172

Gnomad AMI AF: 0.00548

Gnomad AMR AF: 0.0917

Gnomad ASJ AF: 0.114

Gnomad EAS AF: 0.275

Gnomad SAS AF: 0.0859

Gnomad FIN AF: 0.117

Gnomad MID AF: 0.0823

Gnomad NFE AF: 0.0740

Gnomad OTH AF: 0.0852

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.0712 AC: 10842 AN: 152236 Hom.: 594 Cov.: 31 AF XY: 0.0753 AC XY: 5606 AN XY: 74436

Gnomad4 AFR AF: 0.0172

Gnomad4 AMR AF: 0.0920

Gnomad4 ASJ AF: 0.114

Gnomad4 EAS AF: 0.275

Gnomad4 SAS AF: 0.0862

Gnomad4 FIN AF: 0.117

Gnomad4 NFE AF: 0.0740

Gnomad4 OTH AF: 0.0890

Alfa AF: 0.0755 Hom.: 237

Bravo AF: 0.0674

Asia WGS AF: 0.186 AC: 645 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
Cadd	Benign	3.8
Dann	Benign	0.39

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1017920; hg19: chr2-8559180;