5-122741780-C-T

Variant names:

• chr5-122741780-C-T
• rs1460038
• ENST00000719844.1:n.92+103G>A

Variant summary

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

The ENST00000719844.1(LINC02201):​n.92+103G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.485 in 152,018 control chromosomes in the GnomAD database, including 18,309 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 0.49 (18309 hom., cov: 32)
• Consequence: LINC02201 ENST00000719844.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0390
• Publications: 2 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=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.576 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000719844.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02201	ENST00000719844.1		n.92+103G>A		intron	N/A
	LINC02201	ENST00000719851.1		n.86+103G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.485 AC: 73658 AN: 151900 Hom.: 18268 Cov.: 32

Gnomad AFR AF: 0.582

Gnomad AMI AF: 0.553

Gnomad AMR AF: 0.489

Gnomad ASJ AF: 0.428

Gnomad EAS AF: 0.417

Gnomad SAS AF: 0.314

Gnomad FIN AF: 0.542

Gnomad MID AF: 0.433

Gnomad NFE AF: 0.436

Gnomad OTH AF: 0.494

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

GnomAD4 genome AF: 0.485 AC: 73747 AN: 152018 Hom.: 18309 Cov.: 32 AF XY: 0.485 AC XY: 36037 AN XY: 74326

African (AFR) AF: 0.582 AC: 24128 AN: 41452

American (AMR) AF: 0.489 AC: 7473 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.428 AC: 1484 AN: 3470

East Asian (EAS) AF: 0.416 AC: 2147 AN: 5164

South Asian (SAS) AF: 0.314 AC: 1515 AN: 4828

European-Finnish (FIN) AF: 0.542 AC: 5715 AN: 10540

Middle Eastern (MID) AF: 0.435 AC: 127 AN: 292

European-Non Finnish (NFE) AF: 0.436 AC: 29602 AN: 67962

Other (OTH) AF: 0.498 AC: 1053 AN: 2116

Alfa AF: 0.468 Hom.: 2196

Bravo AF: 0.490

Asia WGS AF: 0.398 AC: 1385 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.1
DANN	Benign	0.67
PhyloP100		0.039

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs1460038;

hg19: chr5-122077475;