3-36821489-C-T

Variant names:

• chr3-36821489-C-T
• rs4624519
• ENST00000623207.1:n.104-72G>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 20 publications found

Genes affected

LINC02033 (HGNC:52867): (long intergenic non-protein coding RNA 2033)

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 = 0.442 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000623207.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02033	NR_147141.1		n.106-72G>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02033	ENST00000623207.1	TSL:2	n.104-72G>A		intron	N/A
	LINC02033	ENST00000623312.1	TSL:3	n.-56G>A		upstream_gene	N/A

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

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.300 AC: 3 AN: 10

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.500 AC: 8 AN: 16

Other (OTH) AC: 0 AN: 0

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

African (AFR) AF: 0.447 AC: 18521 AN: 41394

American (AMR) AF: 0.366 AC: 5595 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.297 AC: 1031 AN: 3472

East Asian (EAS) AF: 0.0604 AC: 312 AN: 5162

South Asian (SAS) AF: 0.293 AC: 1408 AN: 4812

European-Finnish (FIN) AF: 0.300 AC: 3161 AN: 10536

Middle Eastern (MID) AF: 0.296 AC: 87 AN: 294

European-Non Finnish (NFE) AF: 0.364 AC: 24746 AN: 67954

Other (OTH) AF: 0.344 AC: 728 AN: 2114

Alfa AF: 0.364 Hom.: 35631

Bravo AF: 0.375

Asia WGS AF: 0.220 AC: 769 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.4
DANN	Benign	0.48
PhyloP100		-0.18

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs4624519;

hg19: chr3-36862980;