chr12-47838389-C-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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02354	XR_007063292.1	n.1359C>T		non_coding_transcript_exon_variant	Exon 3 of 3

Ensembl

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

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 v4.3

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;