rs13359418

Variant names:

• chr5-3688312-T-C
• rs13359418

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.248 AC: 10286 AN: 41514

American (AMR) AF: 0.194 AC: 2956 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.250 AC: 866 AN: 3468

East Asian (EAS) AF: 0.00734 AC: 38 AN: 5180

South Asian (SAS) AF: 0.117 AC: 564 AN: 4820

European-Finnish (FIN) AF: 0.168 AC: 1773 AN: 10584

Middle Eastern (MID) AF: 0.267 AC: 78 AN: 292

European-Non Finnish (NFE) AF: 0.218 AC: 14790 AN: 67978

Other (OTH) AF: 0.229 AC: 482 AN: 2104

Alfa AF: 0.217 Hom.: 1929

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
PhyloP100		0.016

Splicing

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

Other links and lift over

dbSNP: rs13359418; hg19: chr5-3688426;