rs9368570

Variant names:

• chr6-28708416-G-A
• rs9368570
• ENST00000806405.1:n.239+1463C>T

Variant summary

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

The ENST00000806405.1(LINC00533):​n.239+1463C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.293 in 151,826 control chromosomes in the GnomAD database, including 6,901 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 0.29 (6901 hom., cov: 31)
• Consequence: LINC00533 ENST00000806405.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.855
• Publications: 8 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=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.511 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC00533	ENST00000806405.1	n.239+1463C>T		intron_variant	Intron 1 of 1
LINC00533	ENST00000806406.1	n.187+1463C>T		intron_variant	Intron 1 of 1
LINC00533	ENST00000806407.1	n.208+1463C>T		intron_variant	Intron 1 of 1
LINC00533	ENST00000806408.1	n.154+1463C>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.293 AC: 44472 AN: 151708 Hom.: 6898 Cov.: 31

Gnomad AFR AF: 0.278

Gnomad AMI AF: 0.465

Gnomad AMR AF: 0.374

Gnomad ASJ AF: 0.316

Gnomad EAS AF: 0.527

Gnomad SAS AF: 0.342

Gnomad FIN AF: 0.267

Gnomad MID AF: 0.287

Gnomad NFE AF: 0.263

Gnomad OTH AF: 0.312

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

GnomAD4 genome AF: 0.293 AC: 44490 AN: 151826 Hom.: 6901 Cov.: 31 AF XY: 0.298 AC XY: 22131 AN XY: 74194

African (AFR) AF: 0.278 AC: 11508 AN: 41414

American (AMR) AF: 0.374 AC: 5702 AN: 15234

Ashkenazi Jewish (ASJ) AF: 0.316 AC: 1096 AN: 3466

East Asian (EAS) AF: 0.527 AC: 2723 AN: 5166

South Asian (SAS) AF: 0.343 AC: 1649 AN: 4808

European-Finnish (FIN) AF: 0.267 AC: 2803 AN: 10508

Middle Eastern (MID) AF: 0.284 AC: 83 AN: 292

European-Non Finnish (NFE) AF: 0.263 AC: 17849 AN: 67916

Other (OTH) AF: 0.310 AC: 654 AN: 2112

Alfa AF: 0.275 Hom.: 13736

Bravo AF: 0.304

Asia WGS AF: 0.386 AC: 1338 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.97
DANN	Benign	0.56
PhyloP100		-0.85

Splicing

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

Other links and lift over

dbSNP: rs9368570; hg19: chr6-28676193;