rs6416595

Variant names:

• chr15-93825268-G-C
• rs6416595
• ENST00000553818.1:n.195+3712C>G

Your query was ambiguous. Multiple possible variants found:

• 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 ENST00000553818.1(LINC01579):​n.195+3712C>G variant causes a intron 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 ENST00000553818.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.98

Genes affected

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

ENSG00000258627 (HGNC:):

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01579	ENST00000553818.1	n.195+3712C>G		intron_variant	Intron 1 of 3	4
LINC01579	ENST00000557481.6	n.431-4168C>G		intron_variant	Intron 3 of 6	5
ENSG00000258627	ENST00000555468.1	n.-109C>G		upstream_gene_variant		6

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;