rs1490075

Variant names:

• chr3-176704864-C-T
• rs1490075
• ENST00000428516.1:n.199-48133G>A

Variant summary

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

The ENST00000428516.1(LINC01208):​n.199-48133G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.12 in 152,186 control chromosomes in the GnomAD database, including 1,262 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 0.12 (1262 hom., cov: 33)
• Consequence: LINC01208 ENST00000428516.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.964
• Publications: 2 publications found

Genes affected

LINC01208 (HGNC:49639): (long intergenic non-protein coding RNA 1208)

ENSG00000303447 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.75).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.173 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
LINC01208	ENST00000428516.1	n.199-48133G>A		intron_variant	Intron 2 of 4	5
LINC01208	ENST00000657476.1	n.154+15613G>A		intron_variant	Intron 1 of 6
LINC01208	ENST00000794389.1	n.425+15613G>A		intron_variant	Intron 4 of 5

Frequencies

GnomAD3 genomes AF: 0.120 AC: 18246 AN: 152068 Hom.: 1262 Cov.: 33

Gnomad AFR AF: 0.177

Gnomad AMI AF: 0.105

Gnomad AMR AF: 0.105

Gnomad ASJ AF: 0.0922

Gnomad EAS AF: 0.137

Gnomad SAS AF: 0.157

Gnomad FIN AF: 0.0939

Gnomad MID AF: 0.118

Gnomad NFE AF: 0.0905

Gnomad OTH AF: 0.124

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

GnomAD4 genome AF: 0.120 AC: 18267 AN: 152186 Hom.: 1262 Cov.: 33 AF XY: 0.121 AC XY: 9020 AN XY: 74394

African (AFR) AF: 0.177 AC: 7327 AN: 41508

American (AMR) AF: 0.105 AC: 1607 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.0922 AC: 320 AN: 3470

East Asian (EAS) AF: 0.137 AC: 711 AN: 5174

South Asian (SAS) AF: 0.157 AC: 755 AN: 4820

European-Finnish (FIN) AF: 0.0939 AC: 996 AN: 10604

Middle Eastern (MID) AF: 0.116 AC: 34 AN: 292

European-Non Finnish (NFE) AF: 0.0905 AC: 6154 AN: 68006

Other (OTH) AF: 0.126 AC: 267 AN: 2114

Alfa AF: 0.106 Hom.: 1498

Bravo AF: 0.121

Asia WGS AF: 0.167 AC: 578 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.75
CADD	Benign	0.93
DANN	Benign	0.73
PhyloP100		-0.96
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: rs1490075; hg19: chr3-176422652;