rs1460039

Positions:

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

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000669389.1(LINC02201):​n.623T>C variant causes a non coding transcript exon 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 ENST00000669389.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.687

Genes affected

LINC02201 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
LINC02201	NR_109881.1	n.361+6903T>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC02201	ENST00000511194.5	n.360+6903T>C		intron_variant		1
LINC02201	ENST00000669389.1	n.623T>C		non_coding_transcript_exon_variant	5/5
LINC02201	ENST00000514657.2	n.1+6903T>C		intron_variant		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

Gnomad4 AFR AF: 0.569

Gnomad4 AMR AF: 0.489

Gnomad4 ASJ AF: 0.421

Gnomad4 EAS AF: 0.417

Gnomad4 SAS AF: 0.313

Gnomad4 FIN AF: 0.531

Gnomad4 NFE AF: 0.429

Gnomad4 OTH AF: 0.495

Alfa AF: 0.445 Hom.: 4764

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1460039; hg19: chr5-122051006;