3-177688276-A-G

Variant names:

• chr3-177688276-A-G
• rs6803889
• ENST00000423466.2:n.465+688A>G

Variant summary

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

The ENST00000442937.6(LINC00578):​n.428+58721A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.408 in 152,026 control chromosomes in the GnomAD database, including 12,945 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 0.41 (12945 hom., cov: 32)
• Consequence: LINC00578 ENST00000442937.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.611
• Publications: 2 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=-0.54).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.428 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.428+58721A>G		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC00578	ENST00000423466.2	TSL:5	n.465+688A>G		intron	N/A
	LINC00578	ENST00000439009.1	TSL:4	n.148-63635A>G		intron	N/A
	LINC00578	ENST00000442937.6	TSL:3	n.428+58721A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.408 AC: 61985 AN: 151910 Hom.: 12917 Cov.: 32

Gnomad AFR AF: 0.432

Gnomad AMI AF: 0.416

Gnomad AMR AF: 0.366

Gnomad ASJ AF: 0.374

Gnomad EAS AF: 0.248

Gnomad SAS AF: 0.260

Gnomad FIN AF: 0.373

Gnomad MID AF: 0.405

Gnomad NFE AF: 0.432

Gnomad OTH AF: 0.421

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

GnomAD4 genome AF: 0.408 AC: 62056 AN: 152026 Hom.: 12945 Cov.: 32 AF XY: 0.399 AC XY: 29662 AN XY: 74318

African (AFR) AF: 0.432 AC: 17897 AN: 41418

American (AMR) AF: 0.365 AC: 5579 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.374 AC: 1298 AN: 3468

East Asian (EAS) AF: 0.248 AC: 1284 AN: 5180

South Asian (SAS) AF: 0.262 AC: 1263 AN: 4822

European-Finnish (FIN) AF: 0.373 AC: 3939 AN: 10574

Middle Eastern (MID) AF: 0.415 AC: 122 AN: 294

European-Non Finnish (NFE) AF: 0.432 AC: 29397 AN: 67974

Other (OTH) AF: 0.425 AC: 898 AN: 2112

Alfa AF: 0.418 Hom.: 3794

Bravo AF: 0.410

Asia WGS AF: 0.275 AC: 958 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.54
CADD	Benign	13
DANN	Benign	0.55
PhyloP100		0.61

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs6803889;

hg19: chr3-177406064;