ENST00000806405.1:n.240-13848C>T

Variant names:

• chr6-28662914-G-A
• rs13194504
• ENST00000806405.1:n.240-13848C>T

Variant summary

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

The ENST00000806405.1(LINC00533):​n.240-13848C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.05 in 152,178 control chromosomes in the GnomAD database, including 320 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 0.050 (320 hom., cov: 31)
• Consequence: LINC00533 ENST00000806405.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.232
• Publications: 38 publications found

Genes affected

LINC00533 (HGNC:18690): (long intergenic non-protein coding RNA 533)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.68).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0869 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000806405.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC00533	ENST00000806405.1		n.240-13848C>T		intron	N/A
	LINC00533	ENST00000806406.1		n.188-14263C>T		intron	N/A
	LINC00533	ENST00000806407.1		n.209-13858C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0501 AC: 7612 AN: 152060 Hom.: 320 Cov.: 31

Gnomad AFR AF: 0.0143

Gnomad AMI AF: 0.126

Gnomad AMR AF: 0.0199

Gnomad ASJ AF: 0.0205

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.000208

Gnomad FIN AF: 0.0395

Gnomad MID AF: 0.00316

Gnomad NFE AF: 0.0888

Gnomad OTH AF: 0.0321

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

GnomAD4 genome AF: 0.0500 AC: 7607 AN: 152178 Hom.: 320 Cov.: 31 AF XY: 0.0446 AC XY: 3322 AN XY: 74402

African (AFR) AF: 0.0142 AC: 591 AN: 41526

American (AMR) AF: 0.0198 AC: 303 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.0205 AC: 71 AN: 3470

East Asian (EAS) AF: 0.00 AC: 0 AN: 5168

South Asian (SAS) AF: 0.000208 AC: 1 AN: 4814

European-Finnish (FIN) AF: 0.0395 AC: 419 AN: 10596

Middle Eastern (MID) AF: 0.00340 AC: 1 AN: 294

European-Non Finnish (NFE) AF: 0.0888 AC: 6039 AN: 68016

Other (OTH) AF: 0.0317 AC: 67 AN: 2112

Alfa AF: 0.0757 Hom.: 961

Bravo AF: 0.0471

Asia WGS AF: 0.00346 AC: 13 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.68
CADD	Benign	4.7
DANN	Benign	0.92
PhyloP100		0.23

Splicing

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

Other links and lift over

dbSNP: rs13194504; hg19: chr6-28630691;