12-49906641-C-T

Variant names:

• chr12-49906641-C-T
• rs6580724
• ENST00000547954.2:n.406+4000C>T

Variant summary

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

The ENST00000547954.2(LINC02395):​n.406+4000C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.745 in 152,050 control chromosomes in the GnomAD database, including 42,801 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 0.75 (42801 hom., cov: 31)
• Consequence: LINC02395 ENST00000547954.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.347
• Publications: 9 publications found

Genes affected

LINC02395 (HGNC:53322): (long intergenic non-protein coding RNA 2395)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.822 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000547954.2. 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
	LINC02395	ENST00000547954.2	TSL:3	n.406+4000C>T		intron	N/A
	LINC02395	ENST00000551539.2	TSL:4	n.48+2638C>T		intron	N/A
	LINC02395	ENST00000655869.1		n.405+4000C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.745 AC: 113210 AN: 151932 Hom.: 42779 Cov.: 31

Gnomad AFR AF: 0.733

Gnomad AMI AF: 0.806

Gnomad AMR AF: 0.677

Gnomad ASJ AF: 0.898

Gnomad EAS AF: 0.371

Gnomad SAS AF: 0.843

Gnomad FIN AF: 0.727

Gnomad MID AF: 0.839

Gnomad NFE AF: 0.783

Gnomad OTH AF: 0.762

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

GnomAD4 genome AF: 0.745 AC: 113285 AN: 152050 Hom.: 42801 Cov.: 31 AF XY: 0.741 AC XY: 55079 AN XY: 74316

African (AFR) AF: 0.733 AC: 30361 AN: 41448

American (AMR) AF: 0.676 AC: 10331 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.898 AC: 3119 AN: 3472

East Asian (EAS) AF: 0.371 AC: 1917 AN: 5172

South Asian (SAS) AF: 0.844 AC: 4069 AN: 4822

European-Finnish (FIN) AF: 0.727 AC: 7675 AN: 10564

Middle Eastern (MID) AF: 0.837 AC: 246 AN: 294

European-Non Finnish (NFE) AF: 0.783 AC: 53227 AN: 67984

Other (OTH) AF: 0.761 AC: 1608 AN: 2112

Alfa AF: 0.771 Hom.: 166667

Bravo AF: 0.735

Asia WGS AF: 0.686 AC: 2389 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	6.7
DANN	Benign	0.85
PhyloP100		-0.35

Splicing

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

Other links and lift over

dbSNP: rs6580724; hg19: chr12-50300424;