chr15-93825268-G-C

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 1 publications found

Genes affected

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

ENSG00000258627 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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
LINC01579	ENST00000766606.1	n.724-4168C>G		intron_variant	Intron 3 of 4
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

African (AFR) AF: 0.776 AC: 4162 AN: 5364

American (AMR) AF: 0.454 AC: 6811 AN: 14994

Ashkenazi Jewish (ASJ) AF: 0.584 AC: 3342 AN: 5718

East Asian (EAS) AF: 0.430 AC: 3893 AN: 9056

South Asian (SAS) AF: 0.504 AC: 20764 AN: 41176

European-Finnish (FIN) AF: 0.487 AC: 8390 AN: 17240

Middle Eastern (MID) AF: 0.594 AC: 554 AN: 932

European-Non Finnish (NFE) AF: 0.581 AC: 80728 AN: 139056

Other (OTH) AF: 0.563 AC: 6400 AN: 11360

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

African (AFR) AF: 0.764 AC: 31627 AN: 41420

American (AMR) AF: 0.533 AC: 8143 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.592 AC: 2052 AN: 3464

East Asian (EAS) AF: 0.427 AC: 2206 AN: 5162

South Asian (SAS) AF: 0.485 AC: 2335 AN: 4812

European-Finnish (FIN) AF: 0.481 AC: 5074 AN: 10538

Middle Eastern (MID) AF: 0.621 AC: 180 AN: 290

European-Non Finnish (NFE) AF: 0.580 AC: 39311 AN: 67766

Other (OTH) AF: 0.592 AC: 1243 AN: 2100

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
PhyloP100		-2.0

Splicing

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

Other links and lift over

dbSNP: rs6416595; hg19: chr15-94368497;