rs433322

chr16-85890966-A-Gchr16-85890966-A-T

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 0.461 in 152,064 control chromosomes in the GnomAD database, including 17,860 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 0.46 (17860 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.224

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.678 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: 0.461 AC: 70035 AN: 151946 Hom.: 17803 Cov.: 32

Gnomad AFR AF: 0.684

Gnomad AMI AF: 0.344

Gnomad AMR AF: 0.483

Gnomad ASJ AF: 0.418

Gnomad EAS AF: 0.448

Gnomad SAS AF: 0.328

Gnomad FIN AF: 0.317

Gnomad MID AF: 0.551

Gnomad NFE AF: 0.356

Gnomad OTH AF: 0.473

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

GnomAD4 genome AF: 0.461 AC: 70153 AN: 152064 Hom.: 17860 Cov.: 32 AF XY: 0.459 AC XY: 34141 AN XY: 74326

Gnomad4 AFR AF: 0.685

Gnomad4 AMR AF: 0.484

Gnomad4 ASJ AF: 0.418

Gnomad4 EAS AF: 0.447

Gnomad4 SAS AF: 0.330

Gnomad4 FIN AF: 0.317

Gnomad4 NFE AF: 0.356

Gnomad4 OTH AF: 0.478

Alfa AF: 0.382 Hom.: 15582

Bravo AF: 0.486

Asia WGS AF: 0.457 AC: 1588 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
Cadd	Benign	1.7
Dann	Benign	0.24

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs433322; hg19: chr16-85924572;