rs8030172

Variant names:

• chr15-47845301-G-A
• rs8030172
• ENST00000558434.2:n.133-336C>T

Variant summary

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

The ENST00000558434.2(LINC01491):​n.133-336C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.336 in 152,016 control chromosomes in the GnomAD database, including 8,942 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 0.34 (8942 hom., cov: 33)
• Consequence: LINC01491 ENST00000558434.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.441
• Publications: 1 publications found

Genes affected

LINC01491 (HGNC:51148): (long intergenic non-protein coding RNA 1491)

ENSG00000259754 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.377 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC01491	NR_120336.1	n.109-336C>T		intron_variant	Intron 1 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01491	ENST00000558434.2	n.133-336C>T		intron_variant	Intron 1 of 4	3
LINC01491	ENST00000558792.6	n.123-336C>T		intron_variant	Intron 1 of 6	3
LINC01491	ENST00000561238.3	n.145-336C>T		intron_variant	Intron 1 of 3	3

Frequencies

GnomAD3 genomes AF: 0.336 AC: 51004 AN: 151898 Hom.: 8943 Cov.: 33

Gnomad AFR AF: 0.246

Gnomad AMI AF: 0.295

Gnomad AMR AF: 0.327

Gnomad ASJ AF: 0.477

Gnomad EAS AF: 0.310

Gnomad SAS AF: 0.393

Gnomad FIN AF: 0.370

Gnomad MID AF: 0.363

Gnomad NFE AF: 0.379

Gnomad OTH AF: 0.333

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

GnomAD4 genome AF: 0.336 AC: 51021 AN: 152016 Hom.: 8942 Cov.: 33 AF XY: 0.339 AC XY: 25178 AN XY: 74296

African (AFR) AF: 0.245 AC: 10173 AN: 41458

American (AMR) AF: 0.326 AC: 4984 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.477 AC: 1656 AN: 3470

East Asian (EAS) AF: 0.310 AC: 1604 AN: 5172

South Asian (SAS) AF: 0.392 AC: 1892 AN: 4824

European-Finnish (FIN) AF: 0.370 AC: 3899 AN: 10542

Middle Eastern (MID) AF: 0.353 AC: 103 AN: 292

European-Non Finnish (NFE) AF: 0.379 AC: 25737 AN: 67962

Other (OTH) AF: 0.333 AC: 704 AN: 2112

Alfa AF: 0.352 Hom.: 3936

Bravo AF: 0.329

Asia WGS AF: 0.310 AC: 1075 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.62
DANN	Benign	0.71
PhyloP100		-0.44

Splicing

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

Other links and lift over

dbSNP: rs8030172; hg19: chr15-48137498;