ENST00000449581.2:n.164+25645A>G

Variant names:

• chr20-7216184-T-C
• rs1013214
• ENST00000449581.2:n.164+25645A>G

Variant summary

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

The ENST00000449581.2(LINC01428):​n.164+25645A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.794 in 152,144 control chromosomes in the GnomAD database, including 48,153 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 0.79 (48153 hom., cov: 32)
• Consequence: LINC01428 ENST00000449581.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.776
• Publications: 1 publications found

Genes affected

LINC01428 (HGNC:50738): (long intergenic non-protein coding RNA 1428)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.899 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC01428	NR_110609.1	n.164+25645A>G		intron_variant	Intron 3 of 7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01428	ENST00000449581.2	n.164+25645A>G		intron_variant	Intron 3 of 7	1
LINC01428	ENST00000702434.1	n.176-24446A>G		intron_variant	Intron 1 of 2
LINC01428	ENST00000716639.1	n.173+41914A>G		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.794 AC: 120671 AN: 152026 Hom.: 48108 Cov.: 32

Gnomad AFR AF: 0.846

Gnomad AMI AF: 0.859

Gnomad AMR AF: 0.723

Gnomad ASJ AF: 0.868

Gnomad EAS AF: 0.862

Gnomad SAS AF: 0.922

Gnomad FIN AF: 0.769

Gnomad MID AF: 0.905

Gnomad NFE AF: 0.762

Gnomad OTH AF: 0.799

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

GnomAD4 genome AF: 0.794 AC: 120772 AN: 152144 Hom.: 48153 Cov.: 32 AF XY: 0.796 AC XY: 59223 AN XY: 74364

African (AFR) AF: 0.846 AC: 35115 AN: 41502

American (AMR) AF: 0.723 AC: 11048 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.868 AC: 3014 AN: 3472

East Asian (EAS) AF: 0.863 AC: 4462 AN: 5172

South Asian (SAS) AF: 0.922 AC: 4443 AN: 4820

European-Finnish (FIN) AF: 0.769 AC: 8129 AN: 10576

Middle Eastern (MID) AF: 0.901 AC: 265 AN: 294

European-Non Finnish (NFE) AF: 0.762 AC: 51825 AN: 68010

Other (OTH) AF: 0.801 AC: 1688 AN: 2108

Alfa AF: 0.771 Hom.: 65470

Bravo AF: 0.790

Asia WGS AF: 0.895 AC: 3114 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.89
DANN	Benign	0.62
PhyloP100		-0.78

Splicing

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

Other links and lift over

dbSNP: rs1013214; hg19: chr20-7196831;