chr15-93766152-T-C

Variant names:

• chr15-93766152-T-C
• rs4238481
• ENST00000553818.1:n.489-5025A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000553818.1(LINC01579):​n.489-5025A>G variant causes a intron 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 ENST00000553818.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.562
• Publications: 1 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000553818.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01579	ENST00000553818.1	TSL:4	n.489-5025A>G		intron	N/A
	LINC01579	ENST00000557481.6	TSL:5	n.541-5025A>G		intron	N/A

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

African (AFR) AF: 0.135 AC: 5626 AN: 41534

American (AMR) AF: 0.174 AC: 2660 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.147 AC: 509 AN: 3472

East Asian (EAS) AF: 0.254 AC: 1312 AN: 5160

South Asian (SAS) AF: 0.0870 AC: 420 AN: 4826

European-Finnish (FIN) AF: 0.148 AC: 1570 AN: 10598

Middle Eastern (MID) AF: 0.139 AC: 41 AN: 294

European-Non Finnish (NFE) AF: 0.129 AC: 8781 AN: 68014

Other (OTH) AF: 0.155 AC: 328 AN: 2116

Alfa AF: 0.136 Hom.: 1100

Bravo AF: 0.146

Asia WGS AF: 0.156 AC: 541 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.0
DANN	Benign	0.53
PhyloP100		-0.56

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs4238481;

hg19: chr15-94309381;