rs4462445

Variant names:

• chr13-28510867-A-C
• rs4462445

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 0.684 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
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.476 AC: 19380 AN: 40750

American (AMR) AF: 0.663 AC: 10037 AN: 15140

Ashkenazi Jewish (ASJ) AF: 0.775 AC: 2687 AN: 3466

East Asian (EAS) AF: 0.879 AC: 4511 AN: 5134

South Asian (SAS) AF: 0.688 AC: 3291 AN: 4782

European-Finnish (FIN) AF: 0.787 AC: 7832 AN: 9948

Middle Eastern (MID) AF: 0.724 AC: 213 AN: 294

European-Non Finnish (NFE) AF: 0.777 AC: 52399 AN: 67472

Other (OTH) AF: 0.691 AC: 1443 AN: 2088

Alfa AF: 0.748 Hom.: 83640

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
PhyloP100		0.42

Splicing

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

Other links and lift over

dbSNP: rs4462445; hg19: chr13-29085004;