rs3861158

Variant names:

• chr13-84313433-G-A
• rs3861158
• ENST00000653443.1:n.292+71336G>A

Your query was ambiguous. Multiple possible variants found:

• chr13-84313433-G-A
• chr13-84313433-G-C

Variant summary

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

The ENST00000653443.1(ENSG00000288016):​n.292+71336G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.641 in 151,894 control chromosomes in the GnomAD database, including 32,047 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 0.64 (32047 hom., cov: 31)
• Consequence: ENSG00000288016 ENST00000653443.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.311
• Publications: 0 publications found

Genes affected

ENSG00000288016 (HGNC:):

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

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.725 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC00333	NR_046871.1	n.138+71336G>A		intron_variant	Intron 3 of 6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000288016	ENST00000653443.1	n.292+71336G>A		intron_variant	Intron 3 of 4

Frequencies

GnomAD3 genomes AF: 0.641 AC: 97272 AN: 151776 Hom.: 32036 Cov.: 31

Gnomad AFR AF: 0.520

Gnomad AMI AF: 0.660

Gnomad AMR AF: 0.577

Gnomad ASJ AF: 0.683

Gnomad EAS AF: 0.367

Gnomad SAS AF: 0.724

Gnomad FIN AF: 0.707

Gnomad MID AF: 0.710

Gnomad NFE AF: 0.731

Gnomad OTH AF: 0.646

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

GnomAD4 genome AF: 0.641 AC: 97322 AN: 151894 Hom.: 32047 Cov.: 31 AF XY: 0.638 AC XY: 47342 AN XY: 74218

African (AFR) AF: 0.520 AC: 21524 AN: 41408

American (AMR) AF: 0.577 AC: 8787 AN: 15238

Ashkenazi Jewish (ASJ) AF: 0.683 AC: 2367 AN: 3468

East Asian (EAS) AF: 0.367 AC: 1885 AN: 5136

South Asian (SAS) AF: 0.723 AC: 3481 AN: 4814

European-Finnish (FIN) AF: 0.707 AC: 7462 AN: 10560

Middle Eastern (MID) AF: 0.705 AC: 206 AN: 292

European-Non Finnish (NFE) AF: 0.731 AC: 49643 AN: 67956

Other (OTH) AF: 0.647 AC: 1366 AN: 2112

Alfa AF: 0.691 Hom.: 4772

Bravo AF: 0.619

Asia WGS AF: 0.552 AC: 1922 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.93
DANN	Benign	0.54
PhyloP100		-0.31

Splicing

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

Other links and lift over

dbSNP: rs3861158; hg19: chr13-84887568;