12-47838115-C-T

Variant names:

• chr12-47838115-C-T
• rs10783215
• XR_001749114.2:n.816C>T

Variant summary

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

The XR_001749114.2(LINC02354):​n.816C>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 0.523 in 152,098 control chromosomes in the GnomAD database, including 21,221 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 0.52 (21221 hom., cov: 33)
• Consequence: LINC02354 XR_001749114.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.788
• Publications: 13 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=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.593 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000548564.1. You can select a different transcript below to see updated ACMG assignments.

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
	LINC02354	ENST00000548564.1	TSL:4	n.*217C>T		downstream_gene	N/A

Frequencies

GnomAD3 genomes AF: 0.523 AC: 79522 AN: 151980 Hom.: 21189 Cov.: 33

Gnomad AFR AF: 0.599

Gnomad AMI AF: 0.603

Gnomad AMR AF: 0.440

Gnomad ASJ AF: 0.545

Gnomad EAS AF: 0.279

Gnomad SAS AF: 0.529

Gnomad FIN AF: 0.507

Gnomad MID AF: 0.494

Gnomad NFE AF: 0.515

Gnomad OTH AF: 0.519

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

GnomAD4 genome AF: 0.523 AC: 79608 AN: 152098 Hom.: 21221 Cov.: 33 AF XY: 0.521 AC XY: 38734 AN XY: 74342

African (AFR) AF: 0.599 AC: 24852 AN: 41490

American (AMR) AF: 0.440 AC: 6729 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.545 AC: 1890 AN: 3470

East Asian (EAS) AF: 0.280 AC: 1450 AN: 5182

South Asian (SAS) AF: 0.528 AC: 2547 AN: 4820

European-Finnish (FIN) AF: 0.507 AC: 5353 AN: 10552

Middle Eastern (MID) AF: 0.503 AC: 148 AN: 294

European-Non Finnish (NFE) AF: 0.515 AC: 34987 AN: 67974

Other (OTH) AF: 0.521 AC: 1103 AN: 2116

Alfa AF: 0.429 Hom.: 1648

Bravo AF: 0.518

Asia WGS AF: 0.446 AC: 1550 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.73
DANN	Benign	0.31
PhyloP100		-0.79

Splicing

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

Other links and lift over

dbSNP: rs10783215; hg19: chr12-48231898;