ENST00000449581.2:n.164+14997T>G

Variant names:

• chr20-7226832-A-C
• rs4140470
• ENST00000449581.2:n.164+14997T>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+14997T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.46 in 151,910 control chromosomes in the GnomAD database, including 16,423 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 0.46 (16423 hom., cov: 31)
• Consequence: LINC01428 ENST00000449581.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.227
• Publications: 3 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=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.587 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC01428	NR_110609.1	n.164+14997T>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+14997T>G		intron_variant	Intron 3 of 7	1
LINC01428	ENST00000702434.1	n.175+31266T>G		intron_variant	Intron 1 of 2
LINC01428	ENST00000716639.1	n.173+31266T>G		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.460 AC: 69885 AN: 151790 Hom.: 16416 Cov.: 31

Gnomad AFR AF: 0.368

Gnomad AMI AF: 0.589

Gnomad AMR AF: 0.476

Gnomad ASJ AF: 0.478

Gnomad EAS AF: 0.605

Gnomad SAS AF: 0.569

Gnomad FIN AF: 0.487

Gnomad MID AF: 0.526

Gnomad NFE AF: 0.487

Gnomad OTH AF: 0.460

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

GnomAD4 genome AF: 0.460 AC: 69929 AN: 151910 Hom.: 16423 Cov.: 31 AF XY: 0.465 AC XY: 34554 AN XY: 74230

African (AFR) AF: 0.369 AC: 15266 AN: 41414

American (AMR) AF: 0.476 AC: 7266 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.478 AC: 1655 AN: 3462

East Asian (EAS) AF: 0.605 AC: 3112 AN: 5144

South Asian (SAS) AF: 0.569 AC: 2738 AN: 4812

European-Finnish (FIN) AF: 0.487 AC: 5137 AN: 10538

Middle Eastern (MID) AF: 0.517 AC: 151 AN: 292

European-Non Finnish (NFE) AF: 0.487 AC: 33105 AN: 67966

Other (OTH) AF: 0.457 AC: 965 AN: 2110

Alfa AF: 0.451 Hom.: 6790

Bravo AF: 0.454

Asia WGS AF: 0.528 AC: 1838 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	4.9
DANN	Benign	0.72
PhyloP100		0.23

Splicing

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

Other links and lift over

dbSNP: rs4140470; hg19: chr20-7207479;