rs4359308

Variant names:

• chr13-86326268-T-C
• rs4359308

Your query was ambiguous. Multiple possible variants found:

• chr13-86326268-T-C
• chr13-86326268-T-G

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 0.133 in 151,800 control chromosomes in the GnomAD database, including 2,247 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 0.13 (2247 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.295
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.305 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: 0.133 AC: 20167 AN: 151682 Hom.: 2241 Cov.: 31

Gnomad AFR AF: 0.309

Gnomad AMI AF: 0.0307

Gnomad AMR AF: 0.112

Gnomad ASJ AF: 0.103

Gnomad EAS AF: 0.0759

Gnomad SAS AF: 0.0720

Gnomad FIN AF: 0.0402

Gnomad MID AF: 0.123

Gnomad NFE AF: 0.0567

Gnomad OTH AF: 0.139

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

GnomAD4 genome AF: 0.133 AC: 20201 AN: 151800 Hom.: 2247 Cov.: 31 AF XY: 0.131 AC XY: 9692 AN XY: 74184

African (AFR) AF: 0.309 AC: 12785 AN: 41370

American (AMR) AF: 0.112 AC: 1696 AN: 15200

Ashkenazi Jewish (ASJ) AF: 0.103 AC: 358 AN: 3470

East Asian (EAS) AF: 0.0756 AC: 390 AN: 5156

South Asian (SAS) AF: 0.0723 AC: 348 AN: 4816

European-Finnish (FIN) AF: 0.0402 AC: 423 AN: 10530

Middle Eastern (MID) AF: 0.116 AC: 34 AN: 294

European-Non Finnish (NFE) AF: 0.0567 AC: 3851 AN: 67944

Other (OTH) AF: 0.137 AC: 288 AN: 2108

Alfa AF: 0.0353 Hom.: 34

Bravo AF: 0.146

Asia WGS AF: 0.122 AC: 424 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	3.9
DANN	Benign	0.60
PhyloP100		0.29

Splicing

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

Other links and lift over

dbSNP: rs4359308; hg19: chr13-86978523;