rs13355565

chr5-57876878-T-C

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 0.139 in 151,846 control chromosomes in the GnomAD database, including 2,399 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 0.14 (2399 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0290

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.264 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.138 AC: 20977 AN: 151728 Hom.: 2370 Cov.: 30

Gnomad AFR AF: 0.250

Gnomad AMI AF: 0.0175

Gnomad AMR AF: 0.265

Gnomad ASJ AF: 0.0588

Gnomad EAS AF: 0.276

Gnomad SAS AF: 0.114

Gnomad FIN AF: 0.0795

Gnomad MID AF: 0.0696

Gnomad NFE AF: 0.0486

Gnomad OTH AF: 0.133

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

GnomAD4 genome AF: 0.139 AC: 21083 AN: 151846 Hom.: 2399 Cov.: 30 AF XY: 0.142 AC XY: 10510 AN XY: 74234

Gnomad4 AFR AF: 0.252

Gnomad4 AMR AF: 0.265

Gnomad4 ASJ AF: 0.0588

Gnomad4 EAS AF: 0.276

Gnomad4 SAS AF: 0.115

Gnomad4 FIN AF: 0.0795

Gnomad4 NFE AF: 0.0486

Gnomad4 OTH AF: 0.138

Alfa AF: 0.132 Hom.: 393

Bravo AF: 0.162

Asia WGS AF: 0.235 AC: 815 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	3.0
Dann	Benign	0.46

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13355565; hg19: chr5-57172705;