rs4777949

Variant names:

• chr15-93766539-G-A
• rs4777949
• ENST00000553818.1:n.489-5412C>T

Variant summary

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

The ENST00000553818.1(LINC01579):​n.489-5412C>T variant causes a intron 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 ENST00000553818.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.510
• 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=-0.99).
• 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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01579	ENST00000553818.1	n.489-5412C>T		intron_variant	Intron 3 of 3	4
LINC01579	ENST00000557481.6	n.541-5412C>T		intron_variant	Intron 4 of 6	5

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

African (AFR) AF: 0.0785 AC: 3261 AN: 41548

American (AMR) AF: 0.167 AC: 2549 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.145 AC: 502 AN: 3468

East Asian (EAS) AF: 0.251 AC: 1297 AN: 5176

South Asian (SAS) AF: 0.0861 AC: 416 AN: 4830

European-Finnish (FIN) AF: 0.150 AC: 1589 AN: 10594

Middle Eastern (MID) AF: 0.122 AC: 36 AN: 294

European-Non Finnish (NFE) AF: 0.128 AC: 8718 AN: 68010

Other (OTH) AF: 0.142 AC: 300 AN: 2112

Alfa AF: 0.130 Hom.: 1709

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
PhyloP100		-0.51

Splicing

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

Other links and lift over

dbSNP: rs4777949; hg19: chr15-94309768;