ABCF1 p.Gly92Arg

Variant names:

• chr6-30578133-G-C
• NM_001025091.2:c.274G>C
• ABCF1 p.Gly92Arg

Your query was ambiguous. Multiple possible variants found:

• chr6-30578133-G-C
• chr6-30578133-G-A
• chr6-30578133-GGA-CGT
• chr6-30578133-GGA-CGC
• chr6-30578133-GGA-CGG
• chr6-30578133-GGA-AGG

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 2P and 2B. PM2 BP4_Moderate

The NM_001025091.2(ABCF1):​c.274G>C​(p.Gly92Arg) variant causes a missense change. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 13/22 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another nucleotide change resulting in the same amino acid substitution has been previously reported as Uncertain significance in ClinVar.

• Frequency: Genomes: not found (cov: 31)
• Consequence: ABCF1 NM_001025091.2 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 4.75
• Publications: 0 publications found

Genes affected

ABCF1 (HGNC:70): (ATP binding cassette subfamily F member 1) The protein encoded by this gene is a member of the superfamily of ATP-binding cassette (ABC) transporters. ABC proteins transport various molecules across extra- and intra-cellular membranes. ABC genes are divided into seven distinct subfamilies (ABC1, MDR/TAP, MRP, ALD, OABP, GCN20, White). This protein is a member of the GCN20 subfamily. Unlike other members of the superfamily, this protein lacks the transmembrane domains which are characteristic of most ABC transporters. This protein may be regulated by tumor necrosis factor-alpha and play a role in enhancement of protein synthesis and the inflammation process. [provided by RefSeq, Jul 2008]

ACMG classification

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.14792666).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001025091.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ABCF1	NM_001025091.2	MANE Select	c.274G>C	p.Gly92Arg	missense	Exon 4 of 25	NP_001020262.1	A0A1U9X609
	ABCF1	NM_001090.3		c.274G>C	p.Gly92Arg	missense	Exon 4 of 24	NP_001081.1	Q2L6I2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ABCF1	ENST00000326195.13	TSL:1 MANE Select	c.274G>C	p.Gly92Arg	missense	Exon 4 of 25	ENSP00000313603.8	Q8NE71-1
	ABCF1	ENST00000376545.7	TSL:1	c.274G>C	p.Gly92Arg	missense	Exon 4 of 24	ENSP00000365728.3	Q8NE71-2
	ABCF1	ENST00000915359.1		c.277G>C	p.Gly93Arg	missense	Exon 4 of 25	ENSP00000585418.1

Frequencies

GnomAD3 genomes Cov.: 31

GnomAD4 exome Cov.: 34

GnomAD4 genome Cov.: 31

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.13
BayesDel_addAF	Benign	-0.049	T
BayesDel_noAF	Benign	-0.31
CADD	Uncertain	24
DANN	Pathogenic	1.0
DEOGEN2	Benign	0.034	T
Eigen	Benign	0.044
Eigen_PC	Benign	0.15
FATHMM_MKL	Uncertain	0.95	D
M_CAP	Benign	0.035	D
MetaRNN	Benign	0.15	T
MetaSVM	Benign	-1.0	T
MutationAssessor	Benign	0.69	N
PhyloP100		4.7
PrimateAI	Benign	0.47	T
PROVEAN	Benign	-0.16	N
REVEL	Benign	0.077
Sift	Uncertain	0.0090	D
Sift4G	Benign	0.55	T
RBP_binding_hub_radar		0.92
RBP_regulation_power_radar		2.7
Varity_R		0.070
gMVP		0.011
Mutation Taster		=81/19	polymorphism

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

hg19: chr6-30545910;