XR_007063292.1:n.1359C>T

Variant names:

• chr12-47838389-C-T
• rs6580639
• XR_007063292.1:n.1359C>T

Variant summary

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

The XR_007063292.1(LINC02354):​n.1359C>T 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 0.975 in 152,148 control chromosomes in the GnomAD database, including 72,399 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 0.98 (72399 hom., cov: 29)
• Consequence: LINC02354 XR_007063292.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.04
• Publications: 5 publications found

Genes affected

LINC02354 (HGNC:53276): (long intergenic non-protein coding RNA 2354)

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 (EAS) allele frequency at 95% confidence interval = 0.986 is higher than 0.05.

Variant Effect in Transcripts

 

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
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.975 AC: 148302 AN: 152030 Hom.: 72340 Cov.: 29

Gnomad AFR AF: 0.994

Gnomad AMI AF: 0.894

Gnomad AMR AF: 0.978

Gnomad ASJ AF: 0.961

Gnomad EAS AF: 1.00

Gnomad SAS AF: 0.995

Gnomad FIN AF: 0.951

Gnomad MID AF: 0.981

Gnomad NFE AF: 0.966

Gnomad OTH AF: 0.976

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

GnomAD4 genome AF: 0.975 AC: 148420 AN: 152148 Hom.: 72399 Cov.: 29 AF XY: 0.975 AC XY: 72484 AN XY: 74342

African (AFR) AF: 0.994 AC: 41258 AN: 41500

American (AMR) AF: 0.978 AC: 14957 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.961 AC: 3332 AN: 3466

East Asian (EAS) AF: 1.00 AC: 5169 AN: 5170

South Asian (SAS) AF: 0.995 AC: 4781 AN: 4804

European-Finnish (FIN) AF: 0.951 AC: 10065 AN: 10588

Middle Eastern (MID) AF: 0.983 AC: 289 AN: 294

European-Non Finnish (NFE) AF: 0.966 AC: 65688 AN: 68008

Other (OTH) AF: 0.976 AC: 2066 AN: 2116

Alfa AF: 0.972 Hom.: 8497

Bravo AF: 0.977

Asia WGS AF: 0.998 AC: 3470 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	0.47
DANN	Benign	0.49
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs6580639; hg19: chr12-48232172;