rs556837667

Variant names:

• chr22-39045049-A-C
• rs556837667
• NM_145298.6:c.280A>C

Your query was ambiguous. Multiple possible variants found:

• chr22-39045049-A-C
• chr22-39045049-A-G

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The NM_145298.6(APOBEC3F):​c.280A>C​(p.Thr94Pro) variant causes a missense change. The variant was absent in control chromosomes in GnomAD project. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: not found (cov: 30)
• Consequence: APOBEC3F NM_145298.6 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 4.39

Genes affected

APOBEC3F (HGNC:17356): (apolipoprotein B mRNA editing enzyme catalytic subunit 3F) This gene is a member of the cytidine deaminase gene family. It is one of seven related genes or pseudogenes found in a cluster, thought to result from gene duplication, on chromosome 22. Members of the cluster encode proteins that are structurally and functionally related to the C to U RNA-editing cytidine deaminase APOBEC1. It is thought that the proteins may be RNA editing enzymes and have roles in growth or cell cycle control. Alternatively spliced transcript variants encoding different isoforms have been identified. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Uncertain_significance. Variant got 2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
APOBEC3F	NM_145298.6	c.280A>C	p.Thr94Pro	missense_variant	Exon 3 of 7	ENST00000308521.10	NP_660341.2
APOBEC3F	XM_047441184.1	c.280A>C	p.Thr94Pro	missense_variant	Exon 3 of 6		XP_047297140.1
APOBEC3F	XM_047441185.1	c.280A>C	p.Thr94Pro	missense_variant	Exon 3 of 5		XP_047297141.1
APOBEC3F	XM_017028642.3	c.280A>C	p.Thr94Pro	missense_variant	Exon 3 of 5		XP_016884131.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
APOBEC3F	ENST00000308521.10	c.280A>C	p.Thr94Pro	missense_variant	Exon 3 of 7	1	NM_145298.6	ENSP00000309749.5
APOBEC3F	ENST00000491387.1	n.427A>C		non_coding_transcript_exon_variant	Exon 3 of 3	4
APOBEC3F	ENST00000476513.1	n.-135A>C		upstream_gene_variant		3

Frequencies

GnomAD3 genomes Cov.: 30

GnomAD4 exome Cov.: 34

GnomAD4 genome Cov.: 30

Bravo AF: 0.00000378

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Uncertain	0.36
BayesDel_addAF	Uncertain	0.024	T
BayesDel_noAF	Benign	-0.20
CADD	Benign	20
DANN	Uncertain	0.98
DEOGEN2	Benign	0.049	T
Eigen	Benign	0.043
Eigen_PC	Benign	-0.056
FATHMM_MKL	Uncertain	0.89	D
LIST_S2	Benign	0.62	T
M_CAP	Benign	0.054	D
MetaRNN	Uncertain	0.56	D
MetaSVM	Benign	-0.73	T
MutationAssessor	Uncertain	2.3	M
PrimateAI	Benign	0.33	T
PROVEAN	Benign	-1.9	N
REVEL	Uncertain	0.29
Sift	Uncertain	0.0020	D
Sift4G	Uncertain	0.0040	D
Polyphen		0.95	P
Vest4		0.31
MutPred		0.71		Gain of catalytic residue at T94 (P = 0.0441);
MVP		0.74
MPC		0.75
ClinPred		0.75	D
GERP RS		2.3
Varity_R		0.83
gMVP		0.46

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: rs556837667; hg19: chr22-39441054;