ENST00000449581.2:n.117-3960G>A

Variant names:

• chr20-7245836-C-T
• rs6140226
• ENST00000449581.2:n.117-3960G>A

Variant summary

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

The ENST00000449581.2(LINC01428):​n.117-3960G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.396 in 152,080 control chromosomes in the GnomAD database, including 13,452 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 0.40 (13452 hom., cov: 32)
• Consequence: LINC01428 ENST00000449581.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.694
• Publications: 9 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=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.584 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC01428	NR_110609.1	n.117-3960G>A		intron_variant	Intron 2 of 7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01428	ENST00000449581.2	n.117-3960G>A		intron_variant	Intron 2 of 7	1
LINC01428	ENST00000702434.1	n.175+12262G>A		intron_variant	Intron 1 of 2
LINC01428	ENST00000716639.1	n.173+12262G>A		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.397 AC: 60259 AN: 151960 Hom.: 13461 Cov.: 32

Gnomad AFR AF: 0.177

Gnomad AMI AF: 0.518

Gnomad AMR AF: 0.441

Gnomad ASJ AF: 0.448

Gnomad EAS AF: 0.602

Gnomad SAS AF: 0.571

Gnomad FIN AF: 0.489

Gnomad MID AF: 0.509

Gnomad NFE AF: 0.472

Gnomad OTH AF: 0.413

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

GnomAD4 genome AF: 0.396 AC: 60269 AN: 152080 Hom.: 13452 Cov.: 32 AF XY: 0.404 AC XY: 30005 AN XY: 74344

African (AFR) AF: 0.177 AC: 7350 AN: 41492

American (AMR) AF: 0.441 AC: 6730 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.448 AC: 1556 AN: 3470

East Asian (EAS) AF: 0.602 AC: 3113 AN: 5174

South Asian (SAS) AF: 0.571 AC: 2756 AN: 4828

European-Finnish (FIN) AF: 0.489 AC: 5161 AN: 10560

Middle Eastern (MID) AF: 0.497 AC: 146 AN: 294

European-Non Finnish (NFE) AF: 0.472 AC: 32117 AN: 67974

Other (OTH) AF: 0.411 AC: 869 AN: 2114

Alfa AF: 0.443 Hom.: 21039

Bravo AF: 0.383

Asia WGS AF: 0.512 AC: 1781 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.4
DANN	Benign	0.47
PhyloP100		-0.69

Splicing

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

Other links and lift over

dbSNP: rs6140226; hg19: chr20-7226483;