rs4462445

Variant names:

• chr13-28510867-A-C
• rs4462445

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 0.684 in 149,982 control chromosomes in the GnomAD database, including 36,478 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 0.68 (36478 hom., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.425

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.857 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: 0.684 AC: 102543 AN: 149880 Hom.: 36492 Cov.: 29

Gnomad AFR AF: 0.476

Gnomad AMI AF: 0.847

Gnomad AMR AF: 0.663

Gnomad ASJ AF: 0.775

Gnomad EAS AF: 0.879

Gnomad SAS AF: 0.691

Gnomad FIN AF: 0.787

Gnomad MID AF: 0.728

Gnomad NFE AF: 0.777

Gnomad OTH AF: 0.691

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

GnomAD4 genome AF: 0.684 AC: 102562 AN: 149982 Hom.: 36478 Cov.: 29 AF XY: 0.684 AC XY: 50075 AN XY: 73188

Gnomad4 AFR AF: 0.476

Gnomad4 AMR AF: 0.663

Gnomad4 ASJ AF: 0.775

Gnomad4 EAS AF: 0.879

Gnomad4 SAS AF: 0.688

Gnomad4 FIN AF: 0.787

Gnomad4 NFE AF: 0.777

Gnomad4 OTH AF: 0.691

Alfa AF: 0.745 Hom.: 27579

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.32
DANN	Benign	0.53

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4462445; hg19: chr13-29085004;