rs9521501

Variant names:

• chr13-88606424-C-T
• rs9521501
• ENST00000653293.2:n.888+16C>T

Variant summary

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

The ENST00000653293.2(LINC00433):​n.888+16C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.828 in 151,848 control chromosomes in the GnomAD database, including 52,592 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 0.83 (52592 hom., cov: 30)
• Consequence: LINC00433 ENST00000653293.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.292
• Publications: 0 publications found

Genes affected

LINC00433 (HGNC:42768): (long intergenic non-protein coding RNA 433)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.907 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
LINC00433	ENST00000653293.2	n.888+16C>T		intron_variant	Intron 4 of 4
LINC00433	ENST00000715718.1	n.653+16C>T		intron_variant	Intron 6 of 8

Frequencies

GnomAD3 genomes AF: 0.828 AC: 125597 AN: 151728 Hom.: 52538 Cov.: 30

Gnomad AFR AF: 0.915

Gnomad AMI AF: 0.851

Gnomad AMR AF: 0.879

Gnomad ASJ AF: 0.893

Gnomad EAS AF: 0.604

Gnomad SAS AF: 0.836

Gnomad FIN AF: 0.644

Gnomad MID AF: 0.829

Gnomad NFE AF: 0.804

Gnomad OTH AF: 0.857

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

GnomAD4 genome AF: 0.828 AC: 125708 AN: 151848 Hom.: 52592 Cov.: 30 AF XY: 0.823 AC XY: 61026 AN XY: 74182

African (AFR) AF: 0.915 AC: 37907 AN: 41440

American (AMR) AF: 0.879 AC: 13421 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.893 AC: 3098 AN: 3470

East Asian (EAS) AF: 0.604 AC: 3093 AN: 5124

South Asian (SAS) AF: 0.835 AC: 4020 AN: 4814

European-Finnish (FIN) AF: 0.644 AC: 6780 AN: 10520

Middle Eastern (MID) AF: 0.823 AC: 242 AN: 294

European-Non Finnish (NFE) AF: 0.803 AC: 54567 AN: 67912

Other (OTH) AF: 0.858 AC: 1807 AN: 2106

Alfa AF: 0.817 Hom.: 7173

Bravo AF: 0.847

Asia WGS AF: 0.764 AC: 2656 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	4.1
DANN	Benign	0.30
PhyloP100		0.29

Splicing

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

Other links and lift over

dbSNP: rs9521501; hg19: chr13-89258679;