16-52549231-C-T

Variant names:

• chr16-52549231-C-T
• rs4784226

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 0.199 in 152,120 control chromosomes in the GnomAD database, including 3,587 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 0.20 (3587 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.577

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.286 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: 0.199 AC: 30298 AN: 152002 Hom.: 3580 Cov.: 32

Gnomad AFR AF: 0.0657

Gnomad AMI AF: 0.287

Gnomad AMR AF: 0.293

Gnomad ASJ AF: 0.303

Gnomad EAS AF: 0.244

Gnomad SAS AF: 0.190

Gnomad FIN AF: 0.247

Gnomad MID AF: 0.269

Gnomad NFE AF: 0.242

Gnomad OTH AF: 0.233

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

GnomAD4 genome AF: 0.199 AC: 30321 AN: 152120 Hom.: 3587 Cov.: 32 AF XY: 0.201 AC XY: 14971 AN XY: 74370

Gnomad4 AFR AF: 0.0656

Gnomad4 AMR AF: 0.294

Gnomad4 ASJ AF: 0.303

Gnomad4 EAS AF: 0.243

Gnomad4 SAS AF: 0.191

Gnomad4 FIN AF: 0.247

Gnomad4 NFE AF: 0.242

Gnomad4 OTH AF: 0.238

Alfa AF: 0.246 Hom.: 1797

Bravo AF: 0.198

Asia WGS AF: 0.229 AC: 798 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	7.4
DANN	Benign	0.73

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4784226; hg19: chr16-52583143;