rs1904559

Variant names:

• chr12-67704827-C-T
• rs1904559
• ENST00000835137.1:n.474+5689G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000835137.1(LINC02421):​n.474+5689G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.134 in 152,274 control chromosomes in the GnomAD database, including 1,412 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 0.13 (1412 hom., cov: 32)
• Consequence: LINC02421 ENST00000835137.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.216
• Publications: 5 publications found

Genes affected

LINC02421 (HGNC:53351): (long intergenic non-protein coding RNA 2421)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.198 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
LINC02421	ENST00000835137.1	n.474+5689G>A		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.134 AC: 20338 AN: 152156 Hom.: 1403 Cov.: 32

Gnomad AFR AF: 0.128

Gnomad AMI AF: 0.0855

Gnomad AMR AF: 0.137

Gnomad ASJ AF: 0.0956

Gnomad EAS AF: 0.208

Gnomad SAS AF: 0.193

Gnomad FIN AF: 0.143

Gnomad MID AF: 0.0949

Gnomad NFE AF: 0.128

Gnomad OTH AF: 0.131

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

GnomAD4 genome AF: 0.134 AC: 20356 AN: 152274 Hom.: 1412 Cov.: 32 AF XY: 0.136 AC XY: 10145 AN XY: 74462

African (AFR) AF: 0.127 AC: 5294 AN: 41546

American (AMR) AF: 0.138 AC: 2107 AN: 15308

Ashkenazi Jewish (ASJ) AF: 0.0956 AC: 332 AN: 3472

East Asian (EAS) AF: 0.208 AC: 1080 AN: 5180

South Asian (SAS) AF: 0.193 AC: 932 AN: 4822

European-Finnish (FIN) AF: 0.143 AC: 1519 AN: 10608

Middle Eastern (MID) AF: 0.0816 AC: 24 AN: 294

European-Non Finnish (NFE) AF: 0.128 AC: 8701 AN: 68020

Other (OTH) AF: 0.137 AC: 289 AN: 2112

Alfa AF: 0.129 Hom.: 4065

Bravo AF: 0.130

Asia WGS AF: 0.187 AC: 649 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	2.6
DANN	Benign	0.69
PhyloP100		0.22

Splicing

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

Other links and lift over

dbSNP: rs1904559; hg19: chr12-68098607;