5-122706960-A-G

Variant names:

• chr5-122706960-A-G
• rs959300
• ENST00000511194.5:n.361-1491T>C

Variant summary

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

The ENST00000511194.5(LINC02201):​n.361-1491T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.829 in 152,132 control chromosomes in the GnomAD database, including 52,791 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 0.83 (52791 hom., cov: 31)
• Consequence: LINC02201 ENST00000511194.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.474
• 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=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.968 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02201	NR_109881.1	n.362-1491T>C		intron_variant	Intron 4 of 11

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02201	ENST00000511194.5	n.361-1491T>C		intron_variant	Intron 4 of 11	1
LINC02201	ENST00000514657.2	n.2-1491T>C		intron_variant	Intron 1 of 3	3
LINC02201	ENST00000649085.1	n.409-1491T>C		intron_variant	Intron 3 of 8

Frequencies

GnomAD3 genomes AF: 0.829 AC: 125977 AN: 152014 Hom.: 52749 Cov.: 31

Gnomad AFR AF: 0.931

Gnomad AMI AF: 0.793

Gnomad AMR AF: 0.848

Gnomad ASJ AF: 0.763

Gnomad EAS AF: 0.991

Gnomad SAS AF: 0.889

Gnomad FIN AF: 0.811

Gnomad MID AF: 0.810

Gnomad NFE AF: 0.752

Gnomad OTH AF: 0.823

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

GnomAD4 genome AF: 0.829 AC: 126078 AN: 152132 Hom.: 52791 Cov.: 31 AF XY: 0.833 AC XY: 61958 AN XY: 74348

African (AFR) AF: 0.931 AC: 38672 AN: 41538

American (AMR) AF: 0.849 AC: 12985 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.763 AC: 2648 AN: 3472

East Asian (EAS) AF: 0.991 AC: 5118 AN: 5166

South Asian (SAS) AF: 0.888 AC: 4266 AN: 4804

European-Finnish (FIN) AF: 0.811 AC: 8569 AN: 10560

Middle Eastern (MID) AF: 0.806 AC: 237 AN: 294

European-Non Finnish (NFE) AF: 0.752 AC: 51116 AN: 67970

Other (OTH) AF: 0.825 AC: 1744 AN: 2114

Alfa AF: 0.765 Hom.: 19466

Bravo AF: 0.836

Asia WGS AF: 0.941 AC: 3269 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	2.8
DANN	Benign	0.46
PhyloP100		-0.47

Splicing

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

Other links and lift over

dbSNP: rs959300; hg19: chr5-122042655; COSMIC: COSV72528194;