rs270596

chr5-38057626-C-T

Variant summary

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

The NR_147009.1(LINC02107):n.233+28570C>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 0.289 in 151,888 control chromosomes in the GnomAD database, including 6,615 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 0.29 (6615 hom., cov: 32)
• Consequence: LINC02107 NR_147009.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.282

Genes affected

LINC02119 (HGNC:52975): (long intergenic non-protein coding RNA 2119)

LINC02107 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.3 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC02107	NR_147009.1	n.233+28570C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC02119	ENST00000669275.1	n.313+28570C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.289 AC: 43844 AN: 151770 Hom.: 6602 Cov.: 32

Gnomad AFR AF: 0.267

Gnomad AMI AF: 0.355

Gnomad AMR AF: 0.231

Gnomad ASJ AF: 0.243

Gnomad EAS AF: 0.312

Gnomad SAS AF: 0.200

Gnomad FIN AF: 0.454

Gnomad MID AF: 0.263

Gnomad NFE AF: 0.297

Gnomad OTH AF: 0.254

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

GnomAD4 genome AF: 0.289 AC: 43891 AN: 151888 Hom.: 6615 Cov.: 32 AF XY: 0.295 AC XY: 21905 AN XY: 74226

Gnomad4 AFR AF: 0.267

Gnomad4 AMR AF: 0.231

Gnomad4 ASJ AF: 0.243

Gnomad4 EAS AF: 0.312

Gnomad4 SAS AF: 0.202

Gnomad4 FIN AF: 0.454

Gnomad4 NFE AF: 0.297

Gnomad4 OTH AF: 0.252

Alfa AF: 0.286 Hom.: 2863

Bravo AF: 0.272

Asia WGS AF: 0.227 AC: 789 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
Cadd	Benign	6.5
Dann	Benign	0.18

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs270596; hg19: chr5-38057728;