5-122706960-A-G

Position:

• chr5-122706960-A-G

Variant summary

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

The NR_109881.1(LINC02201):​n.362-1491T>C variant causes a intron, non coding transcript 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 NR_109881.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.474

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
LINC02201	NR_109881.1	n.362-1491T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC02201	ENST00000511194.5	n.361-1491T>C		intron_variant, non_coding_transcript_variant		1

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

Gnomad4 AFR AF: 0.931

Gnomad4 AMR AF: 0.849

Gnomad4 ASJ AF: 0.763

Gnomad4 EAS AF: 0.991

Gnomad4 SAS AF: 0.888

Gnomad4 FIN AF: 0.811

Gnomad4 NFE AF: 0.752

Gnomad4 OTH AF: 0.825

Alfa AF: 0.763 Hom.: 16868

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

Splicing

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

Publications

LitVar

Other links and lift over

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