rs13359418

Variant names:

• chr5-3688312-T-C
• rs13359418

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 0.211 in 152,116 control chromosomes in the GnomAD database, including 3,562 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 (3562 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0160

ACMG classification

Verdict is Benign. Variant got -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 = 0.244 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

Frequencies

GnomAD3 genomes AF: 0.211 AC: 32047 AN: 151998 Hom.: 3563 Cov.: 32

Gnomad AFR AF: 0.248

Gnomad AMI AF: 0.231

Gnomad AMR AF: 0.194

Gnomad ASJ AF: 0.250

Gnomad EAS AF: 0.00751

Gnomad SAS AF: 0.117

Gnomad FIN AF: 0.168

Gnomad MID AF: 0.271

Gnomad NFE AF: 0.218

Gnomad OTH AF: 0.232

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

GnomAD4 genome AF: 0.211 AC: 32044 AN: 152116 Hom.: 3562 Cov.: 32 AF XY: 0.205 AC XY: 15268 AN XY: 74370

Gnomad4 AFR AF: 0.248

Gnomad4 AMR AF: 0.194

Gnomad4 ASJ AF: 0.250

Gnomad4 EAS AF: 0.00734

Gnomad4 SAS AF: 0.117

Gnomad4 FIN AF: 0.168

Gnomad4 NFE AF: 0.218

Gnomad4 OTH AF: 0.229

Alfa AF: 0.216 Hom.: 1741

Bravo AF: 0.216

Asia WGS AF: 0.0770 AC: 268 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	1.3
DANN	Benign	0.25

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13359418; hg19: chr5-3688426;