rs2478333

chr13-47588423-C-Achr13-47588423-C-T

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 0.244 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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.244 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

Gnomad4 AFR AF: 0.0626

Gnomad4 AMR AF: 0.243

Gnomad4 ASJ AF: 0.279

Gnomad4 EAS AF: 0.0776

Gnomad4 SAS AF: 0.280

Gnomad4 FIN AF: 0.247

Gnomad4 NFE AF: 0.358

Gnomad4 OTH AF: 0.280

Alfa AF: 0.334 Hom.: 13884

Bravo AF: 0.235

Asia WGS AF: 0.176 AC: 614 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	5.6
Dann	Benign	0.31

Splicing

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

Publications

LitVar

Other links and lift over

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