rs948421

chr8-60491406-T-C

Variant summary

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

The ENST00000530725.6(LINC01301):n.314+17241A>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 0.546 in 151,934 control chromosomes in the GnomAD database, including 26,094 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 0.55 (26094 hom., cov: 31)
• Consequence: LINC01301 ENST00000530725.6 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.528

Genes affected

LINC01301 (HGNC:50464): (long intergenic non-protein coding RNA 1301)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.868 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
LINC01301	ENST00000530725.6	n.314+17241A>G		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.546 AC: 82865 AN: 151820 Hom.: 26042 Cov.: 31

Gnomad AFR AF: 0.875

Gnomad AMI AF: 0.246

Gnomad AMR AF: 0.448

Gnomad ASJ AF: 0.511

Gnomad EAS AF: 0.571

Gnomad SAS AF: 0.626

Gnomad FIN AF: 0.452

Gnomad MID AF: 0.637

Gnomad NFE AF: 0.380

Gnomad OTH AF: 0.535

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

GnomAD4 genome AF: 0.546 AC: 82981 AN: 151934 Hom.: 26094 Cov.: 31 AF XY: 0.549 AC XY: 40722 AN XY: 74238

Gnomad4 AFR AF: 0.875

Gnomad4 AMR AF: 0.448

Gnomad4 ASJ AF: 0.511

Gnomad4 EAS AF: 0.571

Gnomad4 SAS AF: 0.626

Gnomad4 FIN AF: 0.452

Gnomad4 NFE AF: 0.380

Gnomad4 OTH AF: 0.537

Alfa AF: 0.481 Hom.: 3254

Bravo AF: 0.556

Asia WGS AF: 0.653 AC: 2274 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	2.3
Dann	Benign	0.49

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs948421; hg19: chr8-61403965;