rs2065200

Variant names:

• chr13-84436781-C-A
• rs2065200
• ENST00000653443.1:n.410-9158C>A

Variant summary

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

The ENST00000653443.1(ENSG00000288016):​n.410-9158C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.137 in 152,156 control chromosomes in the GnomAD database, including 2,022 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 (2022 hom., cov: 32)
• Consequence: ENSG00000288016 ENST00000653443.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.53
• 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=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.259 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC00333	NR_046871.1	n.139-125583C>A		intron_variant	Intron 3 of 6
LOC105370289	XR_942133.1	n.369-24862G>T		intron_variant	Intron 5 of 5
LOC105370289	XR_942134.1	n.366-24862G>T		intron_variant	Intron 5 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000288016	ENST00000653443.1	n.410-9158C>A		intron_variant	Intron 4 of 4

Frequencies

GnomAD3 genomes AF: 0.137 AC: 20828 AN: 152038 Hom.: 2010 Cov.: 32

Gnomad AFR AF: 0.263

Gnomad AMI AF: 0.0504

Gnomad AMR AF: 0.152

Gnomad ASJ AF: 0.0462

Gnomad EAS AF: 0.209

Gnomad SAS AF: 0.0634

Gnomad FIN AF: 0.0384

Gnomad MID AF: 0.123

Gnomad NFE AF: 0.0787

Gnomad OTH AF: 0.122

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

GnomAD4 genome AF: 0.137 AC: 20881 AN: 152156 Hom.: 2022 Cov.: 32 AF XY: 0.136 AC XY: 10133 AN XY: 74406

African (AFR) AF: 0.263 AC: 10907 AN: 41498

American (AMR) AF: 0.152 AC: 2319 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.0462 AC: 160 AN: 3466

East Asian (EAS) AF: 0.210 AC: 1085 AN: 5158

South Asian (SAS) AF: 0.0639 AC: 308 AN: 4822

European-Finnish (FIN) AF: 0.0384 AC: 407 AN: 10610

Middle Eastern (MID) AF: 0.129 AC: 38 AN: 294

European-Non Finnish (NFE) AF: 0.0787 AC: 5354 AN: 67998

Other (OTH) AF: 0.122 AC: 257 AN: 2112

Alfa AF: 0.0994 Hom.: 1030

Bravo AF: 0.151

Asia WGS AF: 0.157 AC: 545 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.079
DANN	Benign	0.68
PhyloP100		-2.5

Splicing

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

Other links and lift over

dbSNP: rs2065200; hg19: chr13-85010916;