rs4238481

Positions:

• chr15-93766152-T-C

Variant summary

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

The ENST00000557481.6(LINC01579):​n.541-5025A>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 0.14 in 152,222 control chromosomes in the GnomAD database, including 1,586 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 0.14 (1586 hom., cov: 32)
• Consequence: LINC01579 ENST00000557481.6 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.562

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=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.243 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
LINC01579	ENST00000557481.6	n.541-5025A>G		intron_variant, non_coding_transcript_variant		5
LINC01579	ENST00000553818.1	n.489-5025A>G		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.140 AC: 21341 AN: 152104 Hom.: 1588 Cov.: 32

Gnomad AFR AF: 0.136

Gnomad AMI AF: 0.116

Gnomad AMR AF: 0.174

Gnomad ASJ AF: 0.147

Gnomad EAS AF: 0.254

Gnomad SAS AF: 0.0876

Gnomad FIN AF: 0.148

Gnomad MID AF: 0.130

Gnomad NFE AF: 0.129

Gnomad OTH AF: 0.154

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

GnomAD4 genome AF: 0.140 AC: 21353 AN: 152222 Hom.: 1586 Cov.: 32 AF XY: 0.140 AC XY: 10421 AN XY: 74440

Gnomad4 AFR AF: 0.135

Gnomad4 AMR AF: 0.174

Gnomad4 ASJ AF: 0.147

Gnomad4 EAS AF: 0.254

Gnomad4 SAS AF: 0.0870

Gnomad4 FIN AF: 0.148

Gnomad4 NFE AF: 0.129

Gnomad4 OTH AF: 0.155

Alfa AF: 0.134 Hom.: 751

Bravo AF: 0.146

Asia WGS AF: 0.156 AC: 541 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.0
DANN	Benign	0.53

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4238481; hg19: chr15-94309381;