rs1122341

Variant names:

• chr3-55260394-T-C
• rs1122341
• ENST00000654581.1:n.363-25924T>C

Variant summary

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

The ENST00000654581.1(LINC02030):​n.363-25924T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.154 in 152,146 control chromosomes in the GnomAD database, including 2,485 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 0.15 (2485 hom., cov: 32)
• Consequence: LINC02030 ENST00000654581.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.308
• Publications: 4 publications found

Genes affected

LINC02030 (HGNC:52864): (long intergenic non-protein coding RNA 2030)

ENSG00000242775 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.298 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02030	NR_183740.1	n.483+13832T>C		intron_variant	Intron 4 of 6
LINC02030	NR_183741.1	n.772+13832T>C		intron_variant	Intron 6 of 8
LINC02030	NR_183742.1	n.386+13832T>C		intron_variant	Intron 3 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02030	ENST00000654581.1	n.363-25924T>C		intron_variant	Intron 3 of 5
LINC02030	ENST00000662390.1	n.321-25924T>C		intron_variant	Intron 3 of 5
LINC02030	ENST00000670191.1	n.212+13832T>C		intron_variant	Intron 2 of 4

Frequencies

GnomAD3 genomes AF: 0.154 AC: 23423 AN: 152028 Hom.: 2476 Cov.: 32

Gnomad AFR AF: 0.0384

Gnomad AMI AF: 0.221

Gnomad AMR AF: 0.304

Gnomad ASJ AF: 0.168

Gnomad EAS AF: 0.243

Gnomad SAS AF: 0.0765

Gnomad FIN AF: 0.168

Gnomad MID AF: 0.133

Gnomad NFE AF: 0.185

Gnomad OTH AF: 0.183

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

GnomAD4 genome AF: 0.154 AC: 23442 AN: 152146 Hom.: 2485 Cov.: 32 AF XY: 0.155 AC XY: 11561 AN XY: 74368

African (AFR) AF: 0.0383 AC: 1590 AN: 41546

American (AMR) AF: 0.305 AC: 4662 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.168 AC: 583 AN: 3466

East Asian (EAS) AF: 0.244 AC: 1257 AN: 5154

South Asian (SAS) AF: 0.0766 AC: 369 AN: 4820

European-Finnish (FIN) AF: 0.168 AC: 1784 AN: 10600

Middle Eastern (MID) AF: 0.133 AC: 39 AN: 294

European-Non Finnish (NFE) AF: 0.185 AC: 12569 AN: 67974

Other (OTH) AF: 0.183 AC: 387 AN: 2110

Alfa AF: 0.165 Hom.: 378

Bravo AF: 0.163

Asia WGS AF: 0.150 AC: 522 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.2
DANN	Benign	0.64
PhyloP100		0.31

Splicing

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

Other links and lift over

dbSNP: rs1122341; hg19: chr3-55294422;