chr3-36821489-C-T

Position:

• chr3-36821489-C-T

Variant summary

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

The ENST00000623207.1(LINC02033):​n.104-72G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.368 in 151,948 control chromosomes in the GnomAD database, including 10,793 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 0.37 (10791 hom., cov: 31)
  • Exomes 𝑓: 0.42 (2 hom.)
• Consequence: LINC02033 ENST00000623207.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.184

Genes affected

LINC02033 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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 = 0.442 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC02033	NR_147141.1	n.106-72G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC02033	ENST00000623207.1	n.104-72G>A		intron_variant		2

Frequencies

GnomAD3 genomes AF: 0.368 AC: 55847 AN: 151802 Hom.: 10778 Cov.: 31

Gnomad AFR AF: 0.447

Gnomad AMI AF: 0.355

Gnomad AMR AF: 0.366

Gnomad ASJ AF: 0.297

Gnomad EAS AF: 0.0605

Gnomad SAS AF: 0.292

Gnomad FIN AF: 0.300

Gnomad MID AF: 0.313

Gnomad NFE AF: 0.364

Gnomad OTH AF: 0.346

GnomAD4 exome AF: 0.423 AC: 11 AN: 26 Hom.: 2 AF XY: 0.571 AC XY: 8 AN XY: 14

Gnomad4 FIN exome AF: 0.300

Gnomad4 NFE exome AF: 0.500

GnomAD4 genome AF: 0.368 AC: 55913 AN: 151922 Hom.: 10791 Cov.: 31 AF XY: 0.362 AC XY: 26877 AN XY: 74260

Gnomad4 AFR AF: 0.447

Gnomad4 AMR AF: 0.366

Gnomad4 ASJ AF: 0.297

Gnomad4 EAS AF: 0.0604

Gnomad4 SAS AF: 0.293

Gnomad4 FIN AF: 0.300

Gnomad4 NFE AF: 0.364

Gnomad4 OTH AF: 0.344

Alfa AF: 0.360 Hom.: 21470

Bravo AF: 0.375

Asia WGS AF: 0.220 AC: 769 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	1.4
DANN	Benign	0.48

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4624519; hg19: chr3-36862980;