chr13-84480131-G-A

Position:

• chr13-84480131-G-A

Variant summary

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

The NR_046871.1(LINC00333):​n.139-82233G>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 0.165 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, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00700

Genes affected

LINC00333 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
LINC00333	NR_046871.1	n.139-82233G>A		intron_variant, non_coding_transcript_variant
LOC105370289	XR_942134.1	n.365+58348C>T		intron_variant, non_coding_transcript_variant
LOC105370289	XR_942133.1	n.368+58348C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.0821

Gnomad4 AMR AF: 0.165

Gnomad4 ASJ AF: 0.210

Gnomad4 EAS AF: 0.408

Gnomad4 SAS AF: 0.271

Gnomad4 FIN AF: 0.131

Gnomad4 NFE AF: 0.192

Gnomad4 OTH AF: 0.177

Alfa AF: 0.196 Hom.: 2241

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9546711; hg19: chr13-85054266;