rs9284813

Variant names:

• chr3-87103019-A-G
• rs9284813
• ENST00000628435.1:n.305+13412A>G

Variant summary

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

The ENST00000628435.1(LINC00506):​n.305+13412A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.222 in 152,072 control chromosomes in the GnomAD database, including 5,001 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 0.22 (5001 hom., cov: 32)
• Consequence: LINC00506 ENST00000628435.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.658
• Publications: 36 publications found

Genes affected

LINC00506 (HGNC:43557): (long intergenic non-protein coding RNA 506)

ENSG00000300916 (HGNC:):

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 = 0.411 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000628435.1. 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
	LINC00506	NR_104153.1		n.328+13412A>G		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC00506	ENST00000628435.1	TSL:4	n.305+13412A>G		intron	N/A
	LINC00506	ENST00000629052.1	TSL:4	n.479+13412A>G		intron	N/A
	LINC00506	ENST00000630120.3	TSL:4	n.647+13412A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.222 AC: 33745 AN: 151954 Hom.: 4996 Cov.: 32

Gnomad AFR AF: 0.416

Gnomad AMI AF: 0.154

Gnomad AMR AF: 0.168

Gnomad ASJ AF: 0.282

Gnomad EAS AF: 0.240

Gnomad SAS AF: 0.157

Gnomad FIN AF: 0.107

Gnomad MID AF: 0.283

Gnomad NFE AF: 0.135

Gnomad OTH AF: 0.232

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

GnomAD4 genome AF: 0.222 AC: 33773 AN: 152072 Hom.: 5001 Cov.: 32 AF XY: 0.218 AC XY: 16244 AN XY: 74346

African (AFR) AF: 0.416 AC: 17226 AN: 41436

American (AMR) AF: 0.168 AC: 2570 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.282 AC: 977 AN: 3468

East Asian (EAS) AF: 0.241 AC: 1245 AN: 5176

South Asian (SAS) AF: 0.157 AC: 757 AN: 4824

European-Finnish (FIN) AF: 0.107 AC: 1134 AN: 10602

Middle Eastern (MID) AF: 0.291 AC: 85 AN: 292

European-Non Finnish (NFE) AF: 0.135 AC: 9152 AN: 67972

Other (OTH) AF: 0.231 AC: 487 AN: 2108

Alfa AF: 0.164 Hom.: 9816

Bravo AF: 0.239

Asia WGS AF: 0.224 AC: 775 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	4.5
DANN	Benign	0.49
PhyloP100		0.66

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: rs9284813;

hg19: chr3-87152169;

COSMIC: COSV53316856;