3-177511191-T-G

Variant names:

• chr3-177511191-T-G
• rs1353899
• ENST00000439009.1:n.147+69081T>G

Variant summary

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

The ENST00000439009.1(LINC00578):​n.147+69081T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.186 in 152,076 control chromosomes in the GnomAD database, including 2,931 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 0.19 (2931 hom., cov: 32)
• Consequence: LINC00578 ENST00000439009.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0440
• Publications: 6 publications found

Genes affected

LINC00578 (HGNC:43807): (long intergenic non-protein coding RNA 578)

ENSG00000310491 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.256 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000439009.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC00578	NR_047568.1		n.191-28204T>G		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC00578	ENST00000439009.1	TSL:4	n.147+69081T>G		intron	N/A
	LINC00578	ENST00000442937.6	TSL:3	n.191-28204T>G		intron	N/A
	LINC00578	ENST00000656037.1		n.184+69081T>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.186 AC: 28289 AN: 151960 Hom.: 2924 Cov.: 32

Gnomad AFR AF: 0.118

Gnomad AMI AF: 0.215

Gnomad AMR AF: 0.262

Gnomad ASJ AF: 0.121

Gnomad EAS AF: 0.233

Gnomad SAS AF: 0.189

Gnomad FIN AF: 0.272

Gnomad MID AF: 0.136

Gnomad NFE AF: 0.197

Gnomad OTH AF: 0.189

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

GnomAD4 genome AF: 0.186 AC: 28296 AN: 152076 Hom.: 2931 Cov.: 32 AF XY: 0.190 AC XY: 14121 AN XY: 74324

African (AFR) AF: 0.117 AC: 4866 AN: 41484

American (AMR) AF: 0.263 AC: 4012 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.121 AC: 418 AN: 3466

East Asian (EAS) AF: 0.231 AC: 1196 AN: 5172

South Asian (SAS) AF: 0.189 AC: 912 AN: 4822

European-Finnish (FIN) AF: 0.272 AC: 2880 AN: 10574

Middle Eastern (MID) AF: 0.143 AC: 42 AN: 294

European-Non Finnish (NFE) AF: 0.197 AC: 13374 AN: 67962

Other (OTH) AF: 0.189 AC: 400 AN: 2112

Alfa AF: 0.191 Hom.: 11603

Bravo AF: 0.185

Asia WGS AF: 0.233 AC: 810 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	2.2
DANN	Benign	0.65
PhyloP100		-0.044

Splicing

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

Other links and lift over

dbSNP: rs1353899; hg19: chr3-177228979;