rs573872

Variant names:

• chr3-153754374-T-G
• rs573872
• ENST00000488210.1:n.478-23567A>C

Variant summary

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

The ENST00000493214.2(LINC02006):​n.24+8129A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.211 in 152,030 control chromosomes in the GnomAD database, including 3,395 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 0.21 (3395 hom., cov: 32)
• Consequence: LINC02006 ENST00000493214.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.629

Genes affected

LINC02006 (HGNC:52842): (long intergenic non-protein coding RNA 2006)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.223 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02006	NR_146713.1	n.24+8129A>C		intron_variant	Intron 1 of 6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02006	ENST00000488210.1	n.478-23567A>C		intron_variant	Intron 3 of 3	4
LINC02006	ENST00000493214.2	n.24+8129A>C		intron_variant	Intron 1 of 6	2

Frequencies

GnomAD3 genomes AF: 0.211 AC: 32059 AN: 151912 Hom.: 3397 Cov.: 32

Gnomad AFR AF: 0.227

Gnomad AMI AF: 0.134

Gnomad AMR AF: 0.199

Gnomad ASJ AF: 0.211

Gnomad EAS AF: 0.195

Gnomad SAS AF: 0.205

Gnomad FIN AF: 0.224

Gnomad MID AF: 0.244

Gnomad NFE AF: 0.205

Gnomad OTH AF: 0.195

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

GnomAD4 genome AF: 0.211 AC: 32069 AN: 152030 Hom.: 3395 Cov.: 32 AF XY: 0.213 AC XY: 15858 AN XY: 74292

Gnomad4 AFR AF: 0.227

Gnomad4 AMR AF: 0.199

Gnomad4 ASJ AF: 0.211

Gnomad4 EAS AF: 0.195

Gnomad4 SAS AF: 0.206

Gnomad4 FIN AF: 0.224

Gnomad4 NFE AF: 0.205

Gnomad4 OTH AF: 0.193

Alfa AF: 0.207 Hom.: 4335

Bravo AF: 0.210

Asia WGS AF: 0.203 AC: 705 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.80
DANN	Benign	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs573872; hg19: chr3-153472163;