3-177458728-G-A

Position:

• chr3-177458728-G-A

Variant summary

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

The NR_047568.1(LINC00578):​n.190+16618G>A 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 0.267 in 152,172 control chromosomes in the GnomAD database, including 6,017 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 0.27 (6017 hom., cov: 33)
• Consequence: LINC00578 NR_047568.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.217

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=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.394 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC00578	NR_047568.1	n.190+16618G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC00578	ENST00000656037.1	n.184+16618G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.267 AC: 40562 AN: 152054 Hom.: 6001 Cov.: 33

Gnomad AFR AF: 0.399

Gnomad AMI AF: 0.109

Gnomad AMR AF: 0.189

Gnomad ASJ AF: 0.204

Gnomad EAS AF: 0.265

Gnomad SAS AF: 0.227

Gnomad FIN AF: 0.187

Gnomad MID AF: 0.241

Gnomad NFE AF: 0.224

Gnomad OTH AF: 0.263

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

GnomAD4 genome AF: 0.267 AC: 40607 AN: 152172 Hom.: 6017 Cov.: 33 AF XY: 0.264 AC XY: 19640 AN XY: 74424

Gnomad4 AFR AF: 0.400

Gnomad4 AMR AF: 0.189

Gnomad4 ASJ AF: 0.204

Gnomad4 EAS AF: 0.265

Gnomad4 SAS AF: 0.228

Gnomad4 FIN AF: 0.187

Gnomad4 NFE AF: 0.224

Gnomad4 OTH AF: 0.260

Alfa AF: 0.229 Hom.: 4146

Bravo AF: 0.270

Asia WGS AF: 0.240 AC: 837 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.5
DANN	Benign	0.51

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6799682; hg19: chr3-177176516;