rs920891

Variant names:

• chr3-55237208-C-T
• rs920891
• ENST00000654581.1:n.362+3849C>T

Variant summary

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

The ENST00000654581.1(LINC02030):​n.362+3849C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.273 in 152,028 control chromosomes in the GnomAD database, including 5,868 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 0.27 (5868 hom., cov: 32)
• Consequence: LINC02030 ENST00000654581.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.132
• Publications: 4 publications found

Genes affected

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

LOC124906243 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.305 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02030	NR_183740.1	n.352+6351C>T		intron_variant	Intron 3 of 6
LINC02030	NR_183741.1	n.369+3849C>T		intron_variant	Intron 3 of 8
LINC02030	NR_183742.1	n.115-6575C>T		intron_variant	Intron 1 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02030	ENST00000654581.1	n.362+3849C>T		intron_variant	Intron 3 of 5
LINC02030	ENST00000662390.1	n.320+3849C>T		intron_variant	Intron 3 of 5
LINC02030	ENST00000809726.1	n.284+47594C>T		intron_variant	Intron 1 of 2
LINC02030	ENST00000809727.1	n.311+3849C>T		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.273 AC: 41458 AN: 151910 Hom.: 5869 Cov.: 32

Gnomad AFR AF: 0.241

Gnomad AMI AF: 0.232

Gnomad AMR AF: 0.269

Gnomad ASJ AF: 0.312

Gnomad EAS AF: 0.0944

Gnomad SAS AF: 0.277

Gnomad FIN AF: 0.246

Gnomad MID AF: 0.342

Gnomad NFE AF: 0.309

Gnomad OTH AF: 0.286

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

GnomAD4 genome AF: 0.273 AC: 41483 AN: 152028 Hom.: 5868 Cov.: 32 AF XY: 0.267 AC XY: 19831 AN XY: 74302

African (AFR) AF: 0.241 AC: 9983 AN: 41456

American (AMR) AF: 0.269 AC: 4111 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.312 AC: 1082 AN: 3468

East Asian (EAS) AF: 0.0946 AC: 487 AN: 5148

South Asian (SAS) AF: 0.277 AC: 1339 AN: 4826

European-Finnish (FIN) AF: 0.246 AC: 2603 AN: 10574

Middle Eastern (MID) AF: 0.344 AC: 101 AN: 294

European-Non Finnish (NFE) AF: 0.309 AC: 20968 AN: 67952

Other (OTH) AF: 0.283 AC: 598 AN: 2116

Alfa AF: 0.306 Hom.: 4348

Bravo AF: 0.273

Asia WGS AF: 0.173 AC: 601 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	3.0
DANN	Benign	0.72
PhyloP100		-0.13

Splicing

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

Other links and lift over

dbSNP: rs920891; hg19: chr3-55271236;