rs9889937

Positions:

• chr17-18668053-A-C
• chr17-18668053-A-G
• chr17-18668053-A-T

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_001368135.1(FOXO3B):​c.*4256T>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 31)
• Consequence: FOXO3B NM_001368135.1 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.198

Genes affected

FOXO3B (HGNC:3822): (forkhead box O3B) Predicted to enable DNA-binding transcription factor activity and sequence-specific DNA binding activity. Predicted to be involved in regulation of transcription, DNA-templated. Predicted to be located in cytosol. [provided by Alliance of Genome Resources, Apr 2022]

ZNF286B (HGNC:):

ACMG classification

Verdict is Likely_benign. Variant got -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
FOXO3B	NM_001368135.1	c.*4256T>G		3_prime_UTR_variant	4/4	ENST00000395675.7	NP_001355064.1
FOXO3B	NM_001368134.1	c.*4256T>G		3_prime_UTR_variant	4/4		NP_001355063.1
ZNF286B	NR_160540.1	n.433-4826T>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
FOXO3B	ENST00000395675	c.*4256T>G		3_prime_UTR_variant	4/4		NM_001368135.1	ENSP00000499455.1
ZNF286B	ENST00000285274.9	n.347-4826T>G		intron_variant		3
ZNF286B	ENST00000668878.2	n.322-4826T>G		intron_variant

Frequencies

GnomAD3 genomes Cov.: 31

GnomAD4 exome Cov.: 0

GnomAD4 genome Cov.: 31

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	5.0
DANN	Benign	0.29

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs9889937; hg19: chr17-18571366;