rs725332

Variant names:

• chr16-89610380-C-T
• rs725332

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 0.0693 in 152,260 control chromosomes in the GnomAD database, including 462 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 0.069 (462 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.205

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.103 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: 0.0693 AC: 10550 AN: 152142 Hom.: 462 Cov.: 32

Gnomad AFR AF: 0.0186

Gnomad AMI AF: 0.182

Gnomad AMR AF: 0.0445

Gnomad ASJ AF: 0.126

Gnomad EAS AF: 0.00115

Gnomad SAS AF: 0.101

Gnomad FIN AF: 0.0655

Gnomad MID AF: 0.0759

Gnomad NFE AF: 0.105

Gnomad OTH AF: 0.0717

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

GnomAD4 genome AF: 0.0693 AC: 10551 AN: 152260 Hom.: 462 Cov.: 32 AF XY: 0.0675 AC XY: 5023 AN XY: 74446

Gnomad4 AFR AF: 0.0186

Gnomad4 AMR AF: 0.0444

Gnomad4 ASJ AF: 0.126

Gnomad4 EAS AF: 0.00116

Gnomad4 SAS AF: 0.102

Gnomad4 FIN AF: 0.0655

Gnomad4 NFE AF: 0.105

Gnomad4 OTH AF: 0.0710

Alfa AF: 0.0875 Hom.: 84

Bravo AF: 0.0624

Asia WGS AF: 0.0530 AC: 187 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	1.6
DANN	Benign	0.10

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs725332; hg19: chr16-89676788;