ENST00000490357.1:n.103+90015T>A

Variant names:

• chr3-163116513-T-A
• rs9824150
• ENST00000490357.1:n.103+90015T>A

Variant summary

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

The ENST00000490357.1(ENSG00000241168):​n.103+90015T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.177 in 151,958 control chromosomes in the GnomAD database, including 2,897 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 0.18 (2897 hom., cov: 32)
• Consequence: ENSG00000241168 ENST00000490357.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.447
• Publications: 5 publications found

Genes affected

ENSG00000241168 (HGNC:):

LINC01192 (HGNC:37197): (long intergenic non-protein coding RNA 1192)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.302 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000241168	ENST00000490357.1	n.103+90015T>A		intron_variant	Intron 1 of 4	5
LINC01192	ENST00000654609.1	n.1300-6355A>T		intron_variant	Intron 11 of 11
LINC01192	ENST00000655228.1	n.699-6355A>T		intron_variant	Intron 7 of 7

Frequencies

GnomAD3 genomes AF: 0.177 AC: 26919 AN: 151842 Hom.: 2898 Cov.: 32

Gnomad AFR AF: 0.0569

Gnomad AMI AF: 0.363

Gnomad AMR AF: 0.185

Gnomad ASJ AF: 0.186

Gnomad EAS AF: 0.0664

Gnomad SAS AF: 0.315

Gnomad FIN AF: 0.300

Gnomad MID AF: 0.174

Gnomad NFE AF: 0.226

Gnomad OTH AF: 0.166

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

GnomAD4 genome AF: 0.177 AC: 26921 AN: 151958 Hom.: 2897 Cov.: 32 AF XY: 0.182 AC XY: 13482 AN XY: 74242

African (AFR) AF: 0.0567 AC: 2355 AN: 41534

American (AMR) AF: 0.186 AC: 2830 AN: 15240

Ashkenazi Jewish (ASJ) AF: 0.186 AC: 646 AN: 3466

East Asian (EAS) AF: 0.0668 AC: 345 AN: 5166

South Asian (SAS) AF: 0.315 AC: 1519 AN: 4822

European-Finnish (FIN) AF: 0.300 AC: 3163 AN: 10536

Middle Eastern (MID) AF: 0.163 AC: 48 AN: 294

European-Non Finnish (NFE) AF: 0.226 AC: 15336 AN: 67890

Other (OTH) AF: 0.166 AC: 349 AN: 2102

Alfa AF: 0.201 Hom.: 431

Bravo AF: 0.161

Asia WGS AF: 0.179 AC: 621 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.48
DANN	Benign	0.28
PhyloP100		-0.45

Splicing

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

Other links and lift over

dbSNP: rs9824150; hg19: chr3-162834301;