rs8024406

chr15-47792070-T-C

Variant summary

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

The ENST00000653152.1(LINC01491):n.476-820A>G variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.217 in 152,136 control chromosomes in the GnomAD database, including 4,458 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 0.22 (4458 hom., cov: 33)
• Consequence: LINC01491 ENST00000653152.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.297

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.72).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.367 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC01491	ENST00000653152.1	n.476-820A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.217 AC: 32920 AN: 152018 Hom.: 4447 Cov.: 33

Gnomad AFR AF: 0.372

Gnomad AMI AF: 0.0647

Gnomad AMR AF: 0.210

Gnomad ASJ AF: 0.231

Gnomad EAS AF: 0.334

Gnomad SAS AF: 0.192

Gnomad FIN AF: 0.0870

Gnomad MID AF: 0.212

Gnomad NFE AF: 0.137

Gnomad OTH AF: 0.224

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

GnomAD4 genome AF: 0.217 AC: 32970 AN: 152136 Hom.: 4458 Cov.: 33 AF XY: 0.214 AC XY: 15956 AN XY: 74406

Gnomad4 AFR AF: 0.372

Gnomad4 AMR AF: 0.210

Gnomad4 ASJ AF: 0.231

Gnomad4 EAS AF: 0.334

Gnomad4 SAS AF: 0.192

Gnomad4 FIN AF: 0.0870

Gnomad4 NFE AF: 0.137

Gnomad4 OTH AF: 0.228

Alfa AF: 0.158 Hom.: 3516

Bravo AF: 0.230

Asia WGS AF: 0.312 AC: 1082 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.72
Cadd	Benign	10
Dann	Benign	0.88

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs8024406; hg19: chr15-48084267;