rs1460039

Variant names:

• chr5-122715311-A-G
• rs1460039
• ENST00000511194.5:n.360+6903T>C

Your query was ambiguous. Multiple possible variants found:

• chr5-122715311-A-G
• chr5-122715311-A-T

Variant summary

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

The ENST00000511194.5(LINC02201):​n.360+6903T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.478 in 151,994 control chromosomes in the GnomAD database, including 17,734 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 0.48 (17734 hom., cov: 31)
• Consequence: LINC02201 ENST00000511194.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.687
• Publications: 4 publications found

Genes affected

LINC02201 (HGNC:53067): (long intergenic non-protein coding RNA 2201)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.563 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02201	NR_109881.1	n.361+6903T>C		intron_variant	Intron 4 of 11

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02201	ENST00000511194.5	n.360+6903T>C		intron_variant	Intron 4 of 11	1
LINC02201	ENST00000669389.1	n.623T>C		non_coding_transcript_exon_variant	Exon 5 of 5
LINC02201	ENST00000514657.2	n.1+6903T>C		intron_variant	Intron 1 of 3	3

Frequencies

GnomAD3 genomes AF: 0.478 AC: 72533 AN: 151876 Hom.: 17695 Cov.: 31

Gnomad AFR AF: 0.569

Gnomad AMI AF: 0.552

Gnomad AMR AF: 0.488

Gnomad ASJ AF: 0.421

Gnomad EAS AF: 0.418

Gnomad SAS AF: 0.313

Gnomad FIN AF: 0.531

Gnomad MID AF: 0.430

Gnomad NFE AF: 0.429

Gnomad OTH AF: 0.491

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

GnomAD4 genome AF: 0.478 AC: 72617 AN: 151994 Hom.: 17734 Cov.: 31 AF XY: 0.478 AC XY: 35500 AN XY: 74304

African (AFR) AF: 0.569 AC: 23601 AN: 41442

American (AMR) AF: 0.489 AC: 7458 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.421 AC: 1457 AN: 3460

East Asian (EAS) AF: 0.417 AC: 2160 AN: 5176

South Asian (SAS) AF: 0.313 AC: 1509 AN: 4820

European-Finnish (FIN) AF: 0.531 AC: 5603 AN: 10554

Middle Eastern (MID) AF: 0.435 AC: 128 AN: 294

European-Non Finnish (NFE) AF: 0.429 AC: 29153 AN: 67964

Other (OTH) AF: 0.495 AC: 1045 AN: 2112

Alfa AF: 0.448 Hom.: 6068

Bravo AF: 0.483

Asia WGS AF: 0.397 AC: 1381 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	5.5
DANN	Benign	0.89
PhyloP100		-0.69

Splicing

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

Other links and lift over

dbSNP: rs1460039; hg19: chr5-122051006;