rs10516099

Variant names:

• chr5-173578299-C-G
• rs10516099
• ENST00000663273.1:n.25C>G

Variant summary

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

The ENST00000663273.1(LINC02995):​n.25C>G 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 0.0966 in 151,738 control chromosomes in the GnomAD database, including 1,597 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 0.097 (1597 hom., cov: 31)
• Consequence: LINC02995 ENST00000663273.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.277

Genes affected

LINC02995 (HGNC:27744): (long intergenic non-protein coding RNA 2995)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.269 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02995	ENST00000663273.1	n.25C>G		non_coding_transcript_exon_variant	Exon 1 of 2
LINC02995	ENST00000653394.1	n.-230C>G		upstream_gene_variant

Frequencies

GnomAD3 genomes AF: 0.0964 AC: 14615 AN: 151618 Hom.: 1590 Cov.: 31

Gnomad AFR AF: 0.273

Gnomad AMI AF: 0.0198

Gnomad AMR AF: 0.0441

Gnomad ASJ AF: 0.0346

Gnomad EAS AF: 0.000777

Gnomad SAS AF: 0.0366

Gnomad FIN AF: 0.0153

Gnomad MID AF: 0.0411

Gnomad NFE AF: 0.0299

Gnomad OTH AF: 0.0830

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

GnomAD4 genome AF: 0.0966 AC: 14657 AN: 151738 Hom.: 1597 Cov.: 31 AF XY: 0.0933 AC XY: 6918 AN XY: 74138

Gnomad4 AFR AF: 0.274

Gnomad4 AMR AF: 0.0440

Gnomad4 ASJ AF: 0.0346

Gnomad4 EAS AF: 0.000779

Gnomad4 SAS AF: 0.0370

Gnomad4 FIN AF: 0.0153

Gnomad4 NFE AF: 0.0299

Gnomad4 OTH AF: 0.0821

Alfa AF: 0.0664 Hom.: 121

Bravo AF: 0.106

Asia WGS AF: 0.0330 AC: 113 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.7
DANN	Benign	0.33

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10516099; hg19: chr5-173005302;