ENST00000449581.2:n.299-8476A>G

Variant names:

• chr20-7156675-T-C
• rs10485714
• ENST00000449581.2:n.299-8476A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The ENST00000449581.2(LINC01428):​n.299-8476A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0161 in 152,338 control chromosomes in the GnomAD database, including 28 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 0.016 (28 hom., cov: 32)
• Consequence: LINC01428 ENST00000449581.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.190
• Publications: 2 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=-0.84).
• BS1: Variant frequency is greater than expected in population eas. GnomAd4 allele frequency = 0.0161 (2452/152338) while in subpopulation EAS AF = 0.0451 (234/5190). AF 95% confidence interval is 0.0404. There are 28 homozygotes in GnomAd4. There are 1236 alleles in the male GnomAd4 subpopulation. Median coverage is 32. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 28 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC01428	NR_110609.1	n.299-8476A>G		intron_variant	Intron 5 of 7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01428	ENST00000449581.2	n.299-8476A>G		intron_variant	Intron 5 of 7	1
LINC01428	ENST00000716639.1	n.174-8476A>G		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.0161 AC: 2456 AN: 152220 Hom.: 28 Cov.: 32

Gnomad AFR AF: 0.00972

Gnomad AMI AF: 0.00219

Gnomad AMR AF: 0.0206

Gnomad ASJ AF: 0.0153

Gnomad EAS AF: 0.0454

Gnomad SAS AF: 0.0292

Gnomad FIN AF: 0.00960

Gnomad MID AF: 0.0127

Gnomad NFE AF: 0.0168

Gnomad OTH AF: 0.0263

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

GnomAD4 genome AF: 0.0161 AC: 2452 AN: 152338 Hom.: 28 Cov.: 32 AF XY: 0.0166 AC XY: 1236 AN XY: 74508

African (AFR) AF: 0.00972 AC: 404 AN: 41576

American (AMR) AF: 0.0206 AC: 315 AN: 15308

Ashkenazi Jewish (ASJ) AF: 0.0153 AC: 53 AN: 3466

East Asian (EAS) AF: 0.0451 AC: 234 AN: 5190

South Asian (SAS) AF: 0.0292 AC: 141 AN: 4826

European-Finnish (FIN) AF: 0.00960 AC: 102 AN: 10620

Middle Eastern (MID) AF: 0.0102 AC: 3 AN: 294

European-Non Finnish (NFE) AF: 0.0168 AC: 1143 AN: 68030

Other (OTH) AF: 0.0260 AC: 55 AN: 2116

Alfa AF: 0.0163 Hom.: 19

Bravo AF: 0.0165

Asia WGS AF: 0.0340 AC: 118 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	1.3
DANN	Benign	0.68
PhyloP100		-0.19
Mutation Taster		=100/0	polymorphism

Splicing

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

Other links and lift over

dbSNP: rs10485714; hg19: chr20-7137322;