13-88583226-T-C

Variant names:

• chr13-88583226-T-C
• rs9515075
• ENST00000653293.2:n.770-23064T>C

Variant summary

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

The ENST00000653293.2(LINC00433):​n.770-23064T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.641 in 151,666 control chromosomes in the GnomAD database, including 31,677 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 0.64 (31677 hom., cov: 31)
• Consequence: LINC00433 ENST00000653293.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0190
• Publications: 2 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=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.711 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.770-23064T>C		intron_variant	Intron 3 of 4
LINC00433	ENST00000715718.1	n.535-23064T>C		intron_variant	Intron 5 of 8

Frequencies

GnomAD3 genomes AF: 0.641 AC: 97216 AN: 151546 Hom.: 31663 Cov.: 31

Gnomad AFR AF: 0.718

Gnomad AMI AF: 0.610

Gnomad AMR AF: 0.529

Gnomad ASJ AF: 0.673

Gnomad EAS AF: 0.624

Gnomad SAS AF: 0.576

Gnomad FIN AF: 0.578

Gnomad MID AF: 0.687

Gnomad NFE AF: 0.633

Gnomad OTH AF: 0.677

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

GnomAD4 genome AF: 0.641 AC: 97252 AN: 151666 Hom.: 31677 Cov.: 31 AF XY: 0.635 AC XY: 47088 AN XY: 74136

African (AFR) AF: 0.718 AC: 29723 AN: 41408

American (AMR) AF: 0.528 AC: 8010 AN: 15166

Ashkenazi Jewish (ASJ) AF: 0.673 AC: 2333 AN: 3464

East Asian (EAS) AF: 0.624 AC: 3222 AN: 5162

South Asian (SAS) AF: 0.575 AC: 2770 AN: 4820

European-Finnish (FIN) AF: 0.578 AC: 6110 AN: 10574

Middle Eastern (MID) AF: 0.697 AC: 205 AN: 294

European-Non Finnish (NFE) AF: 0.633 AC: 42911 AN: 67764

Other (OTH) AF: 0.671 AC: 1414 AN: 2106

Alfa AF: 0.628 Hom.: 8034

Bravo AF: 0.642

Asia WGS AF: 0.573 AC: 1988 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.6
DANN	Benign	0.47
PhyloP100		-0.019

Splicing

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

Other links and lift over

dbSNP: rs9515075; hg19: chr13-89235481;