rs4500383

Variant names:

• chr1-212218254-C-T
• rs4500383
• ENST00000685933.2:n.153-3478G>A

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000685933.2(LINC02608):​n.153-3478G>A variant causes a intron 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 ENST00000685933.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.215
• Publications: 2 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
LINC02608	NR_125982.1	n.292-3478G>A		intron_variant	Intron 2 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02608	ENST00000685933.2	n.153-3478G>A		intron_variant	Intron 2 of 4
LINC02608	ENST00000771310.1	n.163-3478G>A		intron_variant	Intron 2 of 3
LINC02608	ENST00000771311.1	n.184-3478G>A		intron_variant	Intron 2 of 3

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

African (AFR) AF: 0.388 AC: 16072 AN: 41386

American (AMR) AF: 0.319 AC: 4872 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.314 AC: 1089 AN: 3470

East Asian (EAS) AF: 0.198 AC: 1017 AN: 5148

South Asian (SAS) AF: 0.326 AC: 1575 AN: 4824

European-Finnish (FIN) AF: 0.271 AC: 2857 AN: 10558

Middle Eastern (MID) AF: 0.289 AC: 85 AN: 294

European-Non Finnish (NFE) AF: 0.403 AC: 27412 AN: 67962

Other (OTH) AF: 0.367 AC: 771 AN: 2098

Alfa AF: 0.366 Hom.: 3497

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
PhyloP100		0.21

Splicing

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

Other links and lift over

dbSNP: rs4500383; hg19: chr1-212391596;