rs518590

Variant names:

• chr13-21730960-C-T
• rs518590
• ENST00000794083.1:n.121-3075C>T

Variant summary

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

The ENST00000794083.1(ENSG00000303388):​n.121-3075C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.206 in 152,026 control chromosomes in the GnomAD database, including 3,469 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 (3469 hom., cov: 31)
• Consequence: ENSG00000303388 ENST00000794083.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.333
• Publications: 12 publications found

Genes affected

ENSG00000303388 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.246 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000794083.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

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

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000303388	ENST00000794083.1		n.121-3075C>T		intron	N/A
	ENSG00000303388	ENST00000794085.1		n.107-3075C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.206 AC: 31320 AN: 151908 Hom.: 3464 Cov.: 31

Gnomad AFR AF: 0.250

Gnomad AMI AF: 0.265

Gnomad AMR AF: 0.130

Gnomad ASJ AF: 0.225

Gnomad EAS AF: 0.00174

Gnomad SAS AF: 0.114

Gnomad FIN AF: 0.225

Gnomad MID AF: 0.212

Gnomad NFE AF: 0.214

Gnomad OTH AF: 0.200

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

GnomAD4 genome AF: 0.206 AC: 31340 AN: 152026 Hom.: 3469 Cov.: 31 AF XY: 0.202 AC XY: 14984 AN XY: 74326

African (AFR) AF: 0.250 AC: 10344 AN: 41436

American (AMR) AF: 0.130 AC: 1985 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.225 AC: 780 AN: 3468

East Asian (EAS) AF: 0.00174 AC: 9 AN: 5166

South Asian (SAS) AF: 0.114 AC: 547 AN: 4814

European-Finnish (FIN) AF: 0.225 AC: 2379 AN: 10572

Middle Eastern (MID) AF: 0.224 AC: 66 AN: 294

European-Non Finnish (NFE) AF: 0.214 AC: 14572 AN: 67980

Other (OTH) AF: 0.198 AC: 416 AN: 2102

Alfa AF: 0.206 Hom.: 6301

Bravo AF: 0.203

Asia WGS AF: 0.0720 AC: 251 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	2.3
DANN	Benign	0.73
PhyloP100		-0.33

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs518590;

hg19: chr13-22305099;