rs4777700

Variant names:

• chr15-93774704-A-G
• rs4777700
• ENST00000553818.1:n.489-13577T>C

Variant summary

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

The ENST00000553818.1(LINC01579):​n.489-13577T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.201 in 152,154 control chromosomes in the GnomAD database, including 3,192 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 0.20 (3192 hom., cov: 32)
• Consequence: LINC01579 ENST00000553818.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.91
• 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=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.252 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.489-13577T>C		intron_variant	Intron 3 of 3	4
LINC01579	ENST00000557481.6	n.541-13577T>C		intron_variant	Intron 4 of 6	5

Frequencies

GnomAD3 genomes AF: 0.201 AC: 30517 AN: 152036 Hom.: 3188 Cov.: 32

Gnomad AFR AF: 0.255

Gnomad AMI AF: 0.211

Gnomad AMR AF: 0.210

Gnomad ASJ AF: 0.198

Gnomad EAS AF: 0.253

Gnomad SAS AF: 0.0988

Gnomad FIN AF: 0.168

Gnomad MID AF: 0.149

Gnomad NFE AF: 0.174

Gnomad OTH AF: 0.215

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

GnomAD4 genome AF: 0.201 AC: 30566 AN: 152154 Hom.: 3192 Cov.: 32 AF XY: 0.198 AC XY: 14694 AN XY: 74390

African (AFR) AF: 0.256 AC: 10608 AN: 41492

American (AMR) AF: 0.210 AC: 3216 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.198 AC: 688 AN: 3470

East Asian (EAS) AF: 0.253 AC: 1308 AN: 5174

South Asian (SAS) AF: 0.0985 AC: 476 AN: 4834

European-Finnish (FIN) AF: 0.168 AC: 1775 AN: 10596

Middle Eastern (MID) AF: 0.160 AC: 47 AN: 294

European-Non Finnish (NFE) AF: 0.174 AC: 11803 AN: 67992

Other (OTH) AF: 0.215 AC: 453 AN: 2108

Alfa AF: 0.178 Hom.: 1295

Bravo AF: 0.211

Asia WGS AF: 0.169 AC: 585 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.012
DANN	Benign	0.31
PhyloP100		-1.9

Splicing

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

Other links and lift over

dbSNP: rs4777700; hg19: chr15-94317933;