rs4633732

chr16-86557806-T-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 0.259 in 152,174 control chromosomes in the GnomAD database, including 5,515 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 0.26 (5515 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0330

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.376 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: 0.259 AC: 39419 AN: 152056 Hom.: 5495 Cov.: 33

Gnomad AFR AF: 0.303

Gnomad AMI AF: 0.195

Gnomad AMR AF: 0.365

Gnomad ASJ AF: 0.115

Gnomad EAS AF: 0.390

Gnomad SAS AF: 0.288

Gnomad FIN AF: 0.318

Gnomad MID AF: 0.237

Gnomad NFE AF: 0.197

Gnomad OTH AF: 0.234

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

GnomAD4 genome AF: 0.259 AC: 39481 AN: 152174 Hom.: 5515 Cov.: 33 AF XY: 0.269 AC XY: 19985 AN XY: 74392

Gnomad4 AFR AF: 0.303

Gnomad4 AMR AF: 0.367

Gnomad4 ASJ AF: 0.115

Gnomad4 EAS AF: 0.390

Gnomad4 SAS AF: 0.288

Gnomad4 FIN AF: 0.318

Gnomad4 NFE AF: 0.197

Gnomad4 OTH AF: 0.237

Alfa AF: 0.229 Hom.: 546

Bravo AF: 0.267

Asia WGS AF: 0.341 AC: 1186 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	0.80
Dann	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4633732; hg19: chr16-86591412;