3-177615218-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_047568.1(LINC00578):n.290-14199A>G variant causes a intron, non coding transcript 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 NR_047568.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.106

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC00578	NR_047568.1	n.290-14199A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC00578	ENST00000656037.1	n.185-14199A>G		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.857

Gnomad4 AMR AF: 0.767

Gnomad4 ASJ AF: 0.717

Gnomad4 EAS AF: 0.681

Gnomad4 SAS AF: 0.716

Gnomad4 FIN AF: 0.788

Gnomad4 NFE AF: 0.724

Gnomad4 OTH AF: 0.735

Alfa AF: 0.733 Hom.: 10667

Bravo AF: 0.766

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	3.4
Dann	Benign	0.49

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1466846; hg19: chr3-177333006;