13-47588423-C-A

Variant names:

• chr13-47588423-C-A
• rs2478333

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 0.244 in 152,154 control chromosomes in the GnomAD database, including 5,819 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 0.24 (5819 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.65
• Publications: 18 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.354 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.244 AC: 37138 AN: 152036 Hom.: 5817 Cov.: 33

Gnomad AFR AF: 0.0627

Gnomad AMI AF: 0.536

Gnomad AMR AF: 0.243

Gnomad ASJ AF: 0.279

Gnomad EAS AF: 0.0780

Gnomad SAS AF: 0.280

Gnomad FIN AF: 0.247

Gnomad MID AF: 0.335

Gnomad NFE AF: 0.358

Gnomad OTH AF: 0.278

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

GnomAD4 genome AF: 0.244 AC: 37142 AN: 152154 Hom.: 5819 Cov.: 33 AF XY: 0.239 AC XY: 17766 AN XY: 74374

African (AFR) AF: 0.0626 AC: 2599 AN: 41550

American (AMR) AF: 0.243 AC: 3713 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.279 AC: 968 AN: 3468

East Asian (EAS) AF: 0.0776 AC: 402 AN: 5180

South Asian (SAS) AF: 0.280 AC: 1348 AN: 4816

European-Finnish (FIN) AF: 0.247 AC: 2609 AN: 10580

Middle Eastern (MID) AF: 0.344 AC: 101 AN: 294

European-Non Finnish (NFE) AF: 0.358 AC: 24321 AN: 67956

Other (OTH) AF: 0.280 AC: 592 AN: 2112

Alfa AF: 0.321 Hom.: 28340

Bravo AF: 0.235

Asia WGS AF: 0.176 AC: 614 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	5.6
DANN	Benign	0.31
PhyloP100		1.7

Splicing

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

Other links and lift over

dbSNP: rs2478333; hg19: chr13-48162558; COSMIC: COSV69349404;