chr12-47838310-C-T

Variant names:

• chr12-47838310-C-T
• rs7968585
• XR_007063292.1:n.1280C>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.1280C>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 0.526 in 151,930 control chromosomes in the GnomAD database, including 21,402 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 0.53 (21402 hom., cov: 31)
• Consequence: LINC02354 XR_007063292.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.850
• Publications: 54 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=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.598 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: 0.526 AC: 79781 AN: 151812 Hom.: 21370 Cov.: 31

Gnomad AFR AF: 0.604

Gnomad AMI AF: 0.602

Gnomad AMR AF: 0.445

Gnomad ASJ AF: 0.545

Gnomad EAS AF: 0.277

Gnomad SAS AF: 0.529

Gnomad FIN AF: 0.506

Gnomad MID AF: 0.513

Gnomad NFE AF: 0.516

Gnomad OTH AF: 0.525

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

GnomAD4 genome AF: 0.526 AC: 79867 AN: 151930 Hom.: 21402 Cov.: 31 AF XY: 0.523 AC XY: 38848 AN XY: 74240

African (AFR) AF: 0.604 AC: 25023 AN: 41414

American (AMR) AF: 0.445 AC: 6788 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.545 AC: 1889 AN: 3466

East Asian (EAS) AF: 0.278 AC: 1433 AN: 5156

South Asian (SAS) AF: 0.529 AC: 2542 AN: 4808

European-Finnish (FIN) AF: 0.506 AC: 5337 AN: 10552

Middle Eastern (MID) AF: 0.524 AC: 153 AN: 292

European-Non Finnish (NFE) AF: 0.516 AC: 35043 AN: 67956

Other (OTH) AF: 0.527 AC: 1110 AN: 2106

Alfa AF: 0.525 Hom.: 36873

Bravo AF: 0.521

Asia WGS AF: 0.444 AC: 1544 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.6
DANN	Benign	0.52
PhyloP100		-0.85

Splicing

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

Other links and lift over

dbSNP: rs7968585; hg19: chr12-48232093;