rs12598453

Variant names:

• chr16-54809819-C-G
• rs12598453

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 0.431 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
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.327 AC: 13530 AN: 41420

American (AMR) AF: 0.406 AC: 6198 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.450 AC: 1559 AN: 3468

East Asian (EAS) AF: 0.0364 AC: 188 AN: 5158

South Asian (SAS) AF: 0.249 AC: 1197 AN: 4806

European-Finnish (FIN) AF: 0.571 AC: 6018 AN: 10546

Middle Eastern (MID) AF: 0.463 AC: 136 AN: 294

European-Non Finnish (NFE) AF: 0.521 AC: 35372 AN: 67936

Other (OTH) AF: 0.425 AC: 894 AN: 2106

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
PhyloP100		-0.095

Splicing

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

Other links and lift over

dbSNP: rs12598453; hg19: chr16-54843731;