rs4500383

chr1-212218254-C-T

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The NR_125982.1(LINC02608):n.292-3478G>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 0.369 in 151,912 control chromosomes in the GnomAD database, including 10,570 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 0.37 (10570 hom., cov: 31)
• Consequence: LINC02608 NR_125982.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.215

Genes affected

LINC02608 (HGNC:54052): (long intergenic non-protein coding RNA 2608)

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.3).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.399 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC02608	NR_125982.1	n.292-3478G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC02608	ENST00000685933.1	n.148-3478G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.369 AC: 56043 AN: 151794 Hom.: 10562 Cov.: 31

Gnomad AFR AF: 0.388

Gnomad AMI AF: 0.367

Gnomad AMR AF: 0.320

Gnomad ASJ AF: 0.314

Gnomad EAS AF: 0.197

Gnomad SAS AF: 0.327

Gnomad FIN AF: 0.271

Gnomad MID AF: 0.288

Gnomad NFE AF: 0.403

Gnomad OTH AF: 0.368

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

GnomAD4 genome AF: 0.369 AC: 56084 AN: 151912 Hom.: 10570 Cov.: 31 AF XY: 0.361 AC XY: 26780 AN XY: 74258

Gnomad4 AFR AF: 0.388

Gnomad4 AMR AF: 0.319

Gnomad4 ASJ AF: 0.314

Gnomad4 EAS AF: 0.198

Gnomad4 SAS AF: 0.326

Gnomad4 FIN AF: 0.271

Gnomad4 NFE AF: 0.403

Gnomad4 OTH AF: 0.367

Alfa AF: 0.380 Hom.: 1906

Bravo AF: 0.373

Asia WGS AF: 0.276 AC: 959 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.30
Cadd	Benign	14
Dann	Benign	0.83

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4500383; hg19: chr1-212391596;