16-53528217-G-C

Variant names:

• chr16-53528217-G-C
• rs1111487

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 0.253 in 152,130 control chromosomes in the GnomAD database, including 5,050 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 0.25 (5050 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.02

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.323 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: 0.253 AC: 38501 AN: 152012 Hom.: 5044 Cov.: 32

Gnomad AFR AF: 0.261

Gnomad AMI AF: 0.289

Gnomad AMR AF: 0.331

Gnomad ASJ AF: 0.283

Gnomad EAS AF: 0.190

Gnomad SAS AF: 0.302

Gnomad FIN AF: 0.169

Gnomad MID AF: 0.370

Gnomad NFE AF: 0.243

Gnomad OTH AF: 0.274

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

GnomAD4 genome AF: 0.253 AC: 38533 AN: 152130 Hom.: 5050 Cov.: 32 AF XY: 0.252 AC XY: 18746 AN XY: 74372

Gnomad4 AFR AF: 0.261

Gnomad4 AMR AF: 0.330

Gnomad4 ASJ AF: 0.283

Gnomad4 EAS AF: 0.190

Gnomad4 SAS AF: 0.303

Gnomad4 FIN AF: 0.169

Gnomad4 NFE AF: 0.243

Gnomad4 OTH AF: 0.280

Alfa AF: 0.129 Hom.: 209

Bravo AF: 0.263

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.70
DANN	Benign	0.65

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1111487; hg19: chr16-53562129;