rs275454

Variant names:

• chr5-6815900-G-A
• rs275454
• ENST00000508881.1:n.467-10743G>A

Your query was ambiguous. Multiple possible variants found:

• chr5-6815900-G-A
• chr5-6815900-G-C
• chr5-6815900-G-T

Variant summary

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

The ENST00000508881.1(LINC02236):​n.467-10743G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.393 in 152,044 control chromosomes in the GnomAD database, including 12,079 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 0.39 (12079 hom., cov: 32)
• Consequence: LINC02236 ENST00000508881.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.629
• Publications: 6 publications found

Genes affected

LINC02236 (HGNC:53107): (long intergenic non-protein coding RNA 2236)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.459 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02236	NR_146281.1	n.467-10743G>A		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02236	ENST00000508881.1	n.467-10743G>A		intron_variant	Intron 1 of 1	4
LINC02236	ENST00000648399.1	n.498-10743G>A		intron_variant	Intron 3 of 6
LINC02236	ENST00000691419.2	n.715-10743G>A		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.393 AC: 59651 AN: 151926 Hom.: 12069 Cov.: 32

Gnomad AFR AF: 0.465

Gnomad AMI AF: 0.418

Gnomad AMR AF: 0.379

Gnomad ASJ AF: 0.356

Gnomad EAS AF: 0.216

Gnomad SAS AF: 0.412

Gnomad FIN AF: 0.336

Gnomad MID AF: 0.370

Gnomad NFE AF: 0.374

Gnomad OTH AF: 0.405

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

GnomAD4 genome AF: 0.393 AC: 59704 AN: 152044 Hom.: 12079 Cov.: 32 AF XY: 0.388 AC XY: 28862 AN XY: 74328

African (AFR) AF: 0.465 AC: 19248 AN: 41430

American (AMR) AF: 0.379 AC: 5792 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.356 AC: 1234 AN: 3470

East Asian (EAS) AF: 0.216 AC: 1119 AN: 5180

South Asian (SAS) AF: 0.411 AC: 1981 AN: 4816

European-Finnish (FIN) AF: 0.336 AC: 3558 AN: 10578

Middle Eastern (MID) AF: 0.381 AC: 112 AN: 294

European-Non Finnish (NFE) AF: 0.374 AC: 25425 AN: 67972

Other (OTH) AF: 0.406 AC: 855 AN: 2106

Alfa AF: 0.366 Hom.: 7584

Bravo AF: 0.397

Asia WGS AF: 0.314 AC: 1093 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.61
DANN	Benign	0.53
PhyloP100		-0.63

Splicing

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

Other links and lift over

dbSNP: rs275454; hg19: chr5-6816013;