3-177481372-A-G

Variant names:

• chr3-177481372-A-G
• rs10513754
• ENST00000439009.1:n.147+39262A>G

Variant summary

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

The ENST00000442937.6(LINC00578):​n.190+39262A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.138 in 149,700 control chromosomes in the GnomAD database, including 1,731 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 0.14 (1731 hom., cov: 30)
• Consequence: LINC00578 ENST00000442937.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.388
• Publications: 6 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=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.222 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.190+39262A>G		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC00578	ENST00000439009.1	TSL:4	n.147+39262A>G		intron	N/A
	LINC00578	ENST00000442937.6	TSL:3	n.190+39262A>G		intron	N/A
	LINC00578	ENST00000656037.1		n.184+39262A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.137 AC: 20552 AN: 149636 Hom.: 1726 Cov.: 30

Gnomad AFR AF: 0.226

Gnomad AMI AF: 0.0396

Gnomad AMR AF: 0.104

Gnomad ASJ AF: 0.0753

Gnomad EAS AF: 0.133

Gnomad SAS AF: 0.138

Gnomad FIN AF: 0.0491

Gnomad MID AF: 0.106

Gnomad NFE AF: 0.110

Gnomad OTH AF: 0.124

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

GnomAD4 genome AF: 0.138 AC: 20592 AN: 149700 Hom.: 1731 Cov.: 30 AF XY: 0.135 AC XY: 9868 AN XY: 72992

African (AFR) AF: 0.226 AC: 9178 AN: 40580

American (AMR) AF: 0.104 AC: 1554 AN: 14992

Ashkenazi Jewish (ASJ) AF: 0.0753 AC: 261 AN: 3466

East Asian (EAS) AF: 0.134 AC: 684 AN: 5122

South Asian (SAS) AF: 0.139 AC: 663 AN: 4762

European-Finnish (FIN) AF: 0.0491 AC: 480 AN: 9770

Middle Eastern (MID) AF: 0.112 AC: 32 AN: 286

European-Non Finnish (NFE) AF: 0.110 AC: 7447 AN: 67734

Other (OTH) AF: 0.124 AC: 257 AN: 2080

Alfa AF: 0.117 Hom.: 1171

Bravo AF: 0.146

Asia WGS AF: 0.142 AC: 493 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.1
DANN	Benign	0.50
PhyloP100		-0.39
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs10513754; hg19: chr3-177199160;