rs12598453

Positions:

• chr16-54809819-C-G

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 0.431 in 151,906 control chromosomes in the GnomAD database, including 15,415 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 0.43 (15415 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0950

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.516 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: 0.432 AC: 65507 AN: 151788 Hom.: 15414 Cov.: 31

Gnomad AFR AF: 0.327

Gnomad AMI AF: 0.467

Gnomad AMR AF: 0.407

Gnomad ASJ AF: 0.450

Gnomad EAS AF: 0.0362

Gnomad SAS AF: 0.249

Gnomad FIN AF: 0.571

Gnomad MID AF: 0.430

Gnomad NFE AF: 0.521

Gnomad OTH AF: 0.429

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

GnomAD4 genome AF: 0.431 AC: 65518 AN: 151906 Hom.: 15415 Cov.: 31 AF XY: 0.427 AC XY: 31716 AN XY: 74236

Gnomad4 AFR AF: 0.327

Gnomad4 AMR AF: 0.406

Gnomad4 ASJ AF: 0.450

Gnomad4 EAS AF: 0.0364

Gnomad4 SAS AF: 0.249

Gnomad4 FIN AF: 0.571

Gnomad4 NFE AF: 0.521

Gnomad4 OTH AF: 0.425

Alfa AF: 0.479 Hom.: 2197

Bravo AF: 0.417

Asia WGS AF: 0.142 AC: 497 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.4
DANN	Benign	0.38

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12598453; hg19: chr16-54843731;