rs6416595

Positions:

• chr15-93825268-G-C
• chr15-93825268-G-T

Variant summary

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

The ENST00000557481.6(LINC01579):​n.431-4168C>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 0.574 in 396,626 control chromosomes in the GnomAD database, including 66,864 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 0.61 (29070 hom., cov: 31)
  • Exomes 𝑓: 0.55 (37794 hom.)
• Consequence: LINC01579 ENST00000557481.6 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.98

Genes affected

LINC01579 (HGNC:27519): (long intergenic non-protein coding RNA 1579)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.757 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC01579	ENST00000557481.6	n.431-4168C>G		intron_variant, non_coding_transcript_variant		5
LINC01579	ENST00000553818.1	n.195+3712C>G		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.610 AC: 92489 AN: 151610 Hom.: 29038 Cov.: 31

Gnomad AFR AF: 0.763

Gnomad AMI AF: 0.445

Gnomad AMR AF: 0.534

Gnomad ASJ AF: 0.592

Gnomad EAS AF: 0.427

Gnomad SAS AF: 0.485

Gnomad FIN AF: 0.481

Gnomad MID AF: 0.631

Gnomad NFE AF: 0.580

Gnomad OTH AF: 0.593

GnomAD4 exome AF: 0.551 AC: 135044 AN: 244896 Hom.: 37794 AF XY: 0.550 AC XY: 77911 AN XY: 141626

Gnomad4 AFR exome AF: 0.776

Gnomad4 AMR exome AF: 0.454

Gnomad4 ASJ exome AF: 0.584

Gnomad4 EAS exome AF: 0.430

Gnomad4 SAS exome AF: 0.504

Gnomad4 FIN exome AF: 0.487

Gnomad4 NFE exome AF: 0.581

Gnomad4 OTH exome AF: 0.563

GnomAD4 genome AF: 0.610 AC: 92576 AN: 151730 Hom.: 29070 Cov.: 31 AF XY: 0.602 AC XY: 44678 AN XY: 74180

Gnomad4 AFR AF: 0.764

Gnomad4 AMR AF: 0.533

Gnomad4 ASJ AF: 0.592

Gnomad4 EAS AF: 0.427

Gnomad4 SAS AF: 0.485

Gnomad4 FIN AF: 0.481

Gnomad4 NFE AF: 0.580

Gnomad4 OTH AF: 0.592

Alfa AF: 0.472 Hom.: 1276

Bravo AF: 0.620

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.63
DANN	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6416595; hg19: chr15-94368497;