rs9546711

Variant names:

• chr13-84480131-G-A
• rs9546711
• NR_046871.1:n.139-82233G>A

Variant summary

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

The NR_046871.1(LINC00333):​n.139-82233G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.165 in 151,780 control chromosomes in the GnomAD database, including 2,528 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 0.17 (2528 hom., cov: 31)
• Consequence: LINC00333 NR_046871.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00700
• Publications: 11 publications found

Genes affected

LINC00333 (HGNC:42050): (long intergenic non-protein coding RNA 333)

LOC105370289 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.393 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC00333	NR_046871.1	n.139-82233G>A		intron_variant	Intron 3 of 6
LOC105370289	XR_942133.1	n.368+58348C>T		intron_variant	Intron 5 of 5
LOC105370289	XR_942134.1	n.365+58348C>T		intron_variant	Intron 5 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.165 AC: 25049 AN: 151662 Hom.: 2519 Cov.: 31

Gnomad AFR AF: 0.0822

Gnomad AMI AF: 0.198

Gnomad AMR AF: 0.164

Gnomad ASJ AF: 0.210

Gnomad EAS AF: 0.407

Gnomad SAS AF: 0.272

Gnomad FIN AF: 0.131

Gnomad MID AF: 0.105

Gnomad NFE AF: 0.192

Gnomad OTH AF: 0.177

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

GnomAD4 genome AF: 0.165 AC: 25074 AN: 151780 Hom.: 2528 Cov.: 31 AF XY: 0.166 AC XY: 12302 AN XY: 74172

African (AFR) AF: 0.0821 AC: 3402 AN: 41418

American (AMR) AF: 0.165 AC: 2515 AN: 15198

Ashkenazi Jewish (ASJ) AF: 0.210 AC: 727 AN: 3468

East Asian (EAS) AF: 0.408 AC: 2095 AN: 5136

South Asian (SAS) AF: 0.271 AC: 1306 AN: 4812

European-Finnish (FIN) AF: 0.131 AC: 1380 AN: 10566

Middle Eastern (MID) AF: 0.110 AC: 32 AN: 292

European-Non Finnish (NFE) AF: 0.192 AC: 13063 AN: 67872

Other (OTH) AF: 0.177 AC: 373 AN: 2106

Alfa AF: 0.187 Hom.: 7043

Bravo AF: 0.163

Asia WGS AF: 0.322 AC: 1119 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	3.9
DANN	Benign	0.73
PhyloP100		-0.0070

Splicing

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

Other links and lift over

dbSNP: rs9546711; hg19: chr13-85054266;