ENST00000830465.1:n.183-128C>T

Variant names:

• chr12-67435923-G-A
• rs7969759
• ENST00000830465.1:n.183-128C>T

Variant summary

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

The ENST00000830465.1(LINC02420):​n.183-128C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0706 in 152,200 control chromosomes in the GnomAD database, including 879 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 0.071 (879 hom., cov: 32)
• Consequence: LINC02420 ENST00000830465.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00700
• Publications: 3 publications found

Genes affected

LINC02420 (HGNC:53350): (long intergenic non-protein coding RNA 2420)

LOC105369812 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.213 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000830465.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02420	ENST00000830465.1		n.183-128C>T		intron	N/A
	LINC02420	ENST00000830466.1		n.273-128C>T		intron	N/A
	LINC02420	ENST00000830467.1		n.260-407C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0705 AC: 10722 AN: 152082 Hom.: 875 Cov.: 32

Gnomad AFR AF: 0.172

Gnomad AMI AF: 0.0230

Gnomad AMR AF: 0.122

Gnomad ASJ AF: 0.00548

Gnomad EAS AF: 0.223

Gnomad SAS AF: 0.0358

Gnomad FIN AF: 0.00867

Gnomad MID AF: 0.0316

Gnomad NFE AF: 0.00204

Gnomad OTH AF: 0.0712

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

GnomAD4 genome AF: 0.0706 AC: 10744 AN: 152200 Hom.: 879 Cov.: 32 AF XY: 0.0728 AC XY: 5414 AN XY: 74410

African (AFR) AF: 0.171 AC: 7113 AN: 41482

American (AMR) AF: 0.123 AC: 1875 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.00548 AC: 19 AN: 3468

East Asian (EAS) AF: 0.223 AC: 1154 AN: 5170

South Asian (SAS) AF: 0.0361 AC: 174 AN: 4824

European-Finnish (FIN) AF: 0.00867 AC: 92 AN: 10614

Middle Eastern (MID) AF: 0.0306 AC: 9 AN: 294

European-Non Finnish (NFE) AF: 0.00203 AC: 138 AN: 68034

Other (OTH) AF: 0.0705 AC: 149 AN: 2114

Alfa AF: 0.0381 Hom.: 664

Bravo AF: 0.0873

Asia WGS AF: 0.114 AC: 395 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	2.3
DANN	Benign	0.25
PhyloP100		0.0070

Splicing

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

Other links and lift over

dbSNP: rs7969759; hg19: chr12-67829703;