3-177615218-A-G

Variant names:

• chr3-177615218-A-G
• rs1466846
• ENST00000439009.1:n.148-136693A>G

Variant summary

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

The ENST00000442937.6(LINC00578):​n.290-14199A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.767 in 151,934 control chromosomes in the GnomAD database, including 44,932 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 0.77 (44932 hom., cov: 31)
• Consequence: LINC00578 ENST00000442937.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.106
• Publications: 9 publications found

Genes affected

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

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.849 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000442937.6. 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
	LINC00578	NR_047568.1		n.290-14199A>G		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC00578	ENST00000439009.1	TSL:4	n.148-136693A>G		intron	N/A
	LINC00578	ENST00000442937.6	TSL:3	n.290-14199A>G		intron	N/A
	LINC00578	ENST00000656037.1		n.185-14199A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.767 AC: 116473 AN: 151814 Hom.: 44890 Cov.: 31

Gnomad AFR AF: 0.856

Gnomad AMI AF: 0.716

Gnomad AMR AF: 0.767

Gnomad ASJ AF: 0.717

Gnomad EAS AF: 0.680

Gnomad SAS AF: 0.718

Gnomad FIN AF: 0.788

Gnomad MID AF: 0.696

Gnomad NFE AF: 0.724

Gnomad OTH AF: 0.737

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

GnomAD4 genome AF: 0.767 AC: 116572 AN: 151934 Hom.: 44932 Cov.: 31 AF XY: 0.769 AC XY: 57113 AN XY: 74244

African (AFR) AF: 0.857 AC: 35490 AN: 41432

American (AMR) AF: 0.767 AC: 11711 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.717 AC: 2489 AN: 3470

East Asian (EAS) AF: 0.681 AC: 3501 AN: 5144

South Asian (SAS) AF: 0.716 AC: 3446 AN: 4814

European-Finnish (FIN) AF: 0.788 AC: 8329 AN: 10564

Middle Eastern (MID) AF: 0.711 AC: 209 AN: 294

European-Non Finnish (NFE) AF: 0.724 AC: 49204 AN: 67934

Other (OTH) AF: 0.735 AC: 1544 AN: 2100

Alfa AF: 0.735 Hom.: 19614

Bravo AF: 0.766

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	3.4
DANN	Benign	0.49
PhyloP100		0.11

Splicing

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

Other links and lift over

dbSNP: rs1466846; hg19: chr3-177333006;