rs8030172

Positions:

• chr15-47845301-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000558792.6(LINC01491):​n.123-336C>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 ENST00000558792.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.441

Genes affected

LINC01491 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
LINC01491	NR_120336.1	n.109-336C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC01491	ENST00000558792.6	n.123-336C>T		intron_variant		3
LINC01491	ENST00000561238.2	n.133-336C>T		intron_variant		3
LINC01491	ENST00000651940.1	n.114+828C>T		intron_variant

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

Gnomad4 AFR AF: 0.245

Gnomad4 AMR AF: 0.326

Gnomad4 ASJ AF: 0.477

Gnomad4 EAS AF: 0.310

Gnomad4 SAS AF: 0.392

Gnomad4 FIN AF: 0.370

Gnomad4 NFE AF: 0.379

Gnomad4 OTH AF: 0.333

Alfa AF: 0.356 Hom.: 2321

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs8030172; hg19: chr15-48137498;