chr12-47838310-C-T

Position:

• chr12-47838310-C-T

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

LINC02354 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
LINC02354	XR_007063292.1	n.1280C>T		non_coding_transcript_exon_variant	3/3
		n.47838310C>T		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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

Gnomad4 AFR AF: 0.604

Gnomad4 AMR AF: 0.445

Gnomad4 ASJ AF: 0.545

Gnomad4 EAS AF: 0.278

Gnomad4 SAS AF: 0.529

Gnomad4 FIN AF: 0.506

Gnomad4 NFE AF: 0.516

Gnomad4 OTH AF: 0.527

Alfa AF: 0.520 Hom.: 24741

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7968585; hg19: chr12-48232093;