12-47838310-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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02354	XR_007063292.1	n.1280C>T		non_coding_transcript_exon_variant	Exon 3 of 3
LINC02354	XR_001749114.2	n.*185C>T		downstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

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 v4.3

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;