rs518590

Positions:

• chr13-21730960-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

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: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.333

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

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

Gnomad4 AFR AF: 0.250

Gnomad4 AMR AF: 0.130

Gnomad4 ASJ AF: 0.225

Gnomad4 EAS AF: 0.00174

Gnomad4 SAS AF: 0.114

Gnomad4 FIN AF: 0.225

Gnomad4 NFE AF: 0.214

Gnomad4 OTH AF: 0.198

Alfa AF: 0.204 Hom.: 4117

Bravo AF: 0.203

Asia WGS AF: 0.0720 AC: 251 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs518590; hg19: chr13-22305099;