rs433322

Variant names:

• chr16-85890966-A-G
• rs433322

Your query was ambiguous. Multiple possible variants found:

• chr16-85890966-A-G
• chr16-85890966-A-T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 6 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.685 AC: 28390 AN: 41450

American (AMR) AF: 0.484 AC: 7386 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.418 AC: 1453 AN: 3472

East Asian (EAS) AF: 0.447 AC: 2318 AN: 5184

South Asian (SAS) AF: 0.330 AC: 1593 AN: 4826

European-Finnish (FIN) AF: 0.317 AC: 3347 AN: 10574

Middle Eastern (MID) AF: 0.541 AC: 159 AN: 294

European-Non Finnish (NFE) AF: 0.356 AC: 24185 AN: 67968

Other (OTH) AF: 0.478 AC: 1008 AN: 2108

Alfa AF: 0.393 Hom.: 21101

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
PhyloP100		-0.22

Splicing

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

Other links and lift over

dbSNP: rs433322; hg19: chr16-85924572;