rs4777949

Positions:

• chr15-93766539-G-A

Variant summary

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

The ENST00000557481.6(LINC01579):​n.541-5412C>T 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 0.123 in 152,246 control chromosomes in the GnomAD database, including 1,285 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 0.12 (1285 hom., cov: 33)
• Consequence: LINC01579 ENST00000557481.6 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.510

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=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.239 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.541-5412C>T		intron_variant, non_coding_transcript_variant		5
LINC01579	ENST00000553818.1	n.489-5412C>T		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.123 AC: 18778 AN: 152128 Hom.: 1287 Cov.: 33

Gnomad AFR AF: 0.0785

Gnomad AMI AF: 0.130

Gnomad AMR AF: 0.166

Gnomad ASJ AF: 0.145

Gnomad EAS AF: 0.251

Gnomad SAS AF: 0.0867

Gnomad FIN AF: 0.150

Gnomad MID AF: 0.114

Gnomad NFE AF: 0.128

Gnomad OTH AF: 0.141

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

GnomAD4 genome AF: 0.123 AC: 18787 AN: 152246 Hom.: 1285 Cov.: 33 AF XY: 0.124 AC XY: 9241 AN XY: 74432

Gnomad4 AFR AF: 0.0785

Gnomad4 AMR AF: 0.167

Gnomad4 ASJ AF: 0.145

Gnomad4 EAS AF: 0.251

Gnomad4 SAS AF: 0.0861

Gnomad4 FIN AF: 0.150

Gnomad4 NFE AF: 0.128

Gnomad4 OTH AF: 0.142

Alfa AF: 0.131 Hom.: 1323

Bravo AF: 0.127

Asia WGS AF: 0.151 AC: 523 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.2
DANN	Benign	0.77

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4777949; hg19: chr15-94309768;