5-122709793-T-C

Variant names:

• chr5-122709793-T-C
• rs2125856
• ENST00000511194.5:n.361-4324A>G

Variant summary

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

The ENST00000511194.5(LINC02201):​n.361-4324A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.305 in 152,046 control chromosomes in the GnomAD database, including 7,570 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 0.31 (7570 hom., cov: 32)
• Consequence: LINC02201 ENST00000511194.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.173
• Publications: 1 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=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.554 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02201	NR_109881.1	n.362-4324A>G		intron_variant	Intron 4 of 11

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02201	ENST00000511194.5	n.361-4324A>G		intron_variant	Intron 4 of 11	1
LINC02201	ENST00000514657.2	n.2-4324A>G		intron_variant	Intron 1 of 3	3
LINC02201	ENST00000649085.1	n.346-714A>G		intron_variant	Intron 2 of 8

Frequencies

GnomAD3 genomes AF: 0.305 AC: 46376 AN: 151928 Hom.: 7568 Cov.: 32

Gnomad AFR AF: 0.263

Gnomad AMI AF: 0.221

Gnomad AMR AF: 0.330

Gnomad ASJ AF: 0.320

Gnomad EAS AF: 0.570

Gnomad SAS AF: 0.544

Gnomad FIN AF: 0.272

Gnomad MID AF: 0.335

Gnomad NFE AF: 0.294

Gnomad OTH AF: 0.290

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

GnomAD4 genome AF: 0.305 AC: 46392 AN: 152046 Hom.: 7570 Cov.: 32 AF XY: 0.312 AC XY: 23159 AN XY: 74308

African (AFR) AF: 0.263 AC: 10920 AN: 41496

American (AMR) AF: 0.329 AC: 5032 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.320 AC: 1111 AN: 3470

East Asian (EAS) AF: 0.571 AC: 2944 AN: 5152

South Asian (SAS) AF: 0.544 AC: 2621 AN: 4820

European-Finnish (FIN) AF: 0.272 AC: 2871 AN: 10570

Middle Eastern (MID) AF: 0.327 AC: 96 AN: 294

European-Non Finnish (NFE) AF: 0.294 AC: 19986 AN: 67946

Other (OTH) AF: 0.288 AC: 609 AN: 2114

Alfa AF: 0.313 Hom.: 3677

Bravo AF: 0.302

Asia WGS AF: 0.519 AC: 1794 AN: 3462

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.1
DANN	Benign	0.53
PhyloP100		0.17

Splicing

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

Other links and lift over

dbSNP: rs2125856; hg19: chr5-122045488; COSMIC: COSV72528199;