NM_001025091.2:c.62C>G

Variant names:

• chr6-30571549-C-G
• rs376093203
• NM_001025091.2:c.62C>G

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2 BP4_Moderate

The NM_001025091.2(ABCF1):​c.62C>G​(p.Thr21Arg) variant causes a missense 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. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. T21M) has been classified as Uncertain significance.

• Frequency:
  • Genomes: not found (cov: 32)
  • Exomes 𝑓: 6.9e-7 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: ABCF1 NM_001025091.2 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.16

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

Verdict is Uncertain_significance. Variant got 0 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.15206987).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ABCF1	NM_001025091.2	c.62C>G	p.Thr21Arg	missense_variant	Exon 1 of 25	ENST00000326195.13	NP_001020262.1
ABCF1	NM_001090.3	c.62C>G	p.Thr21Arg	missense_variant	Exon 1 of 24		NP_001081.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ABCF1	ENST00000326195.13	c.62C>G	p.Thr21Arg	missense_variant	Exon 1 of 25	1	NM_001025091.2	ENSP00000313603.8
ABCF1	ENST00000376545.7	c.62C>G	p.Thr21Arg	missense_variant	Exon 1 of 24	1		ENSP00000365728.3
ABCF1	ENST00000441867.6	c.62C>G	p.Thr21Arg	missense_variant	Exon 1 of 25	5		ENSP00000405512.2
ABCF1	ENST00000468958.1	c.-183C>G		5_prime_UTR_variant	Exon 1 of 7	3		ENSP00000440893.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD3 exomes AF: 0.00000419 AC: 1 AN: 238914 Hom.: 0 AF XY: 0.00 AC XY: 0 AN XY: 131024

Gnomad AFR exome AF: 0.00

Gnomad AMR exome AF: 0.00

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.00

Gnomad SAS exome AF: 0.0000334

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.00

Gnomad OTH exome AF: 0.00

GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 6.86e-7 AC: 1 AN: 1457846 Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0 AN XY: 725024

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.0000116

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Cov.: 32

ExAC AF: 0.00000852 AC: 1

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.12
BayesDel_addAF	Benign	-0.026	T
BayesDel_noAF	Benign	-0.17
CADD	Uncertain	23
DANN	Uncertain	0.98
DEOGEN2	Benign	0.031	T;.;T
Eigen	Benign	-0.57
Eigen_PC	Benign	-0.48
FATHMM_MKL	Benign	0.56	D
M_CAP	Uncertain	0.20	D
MetaRNN	Benign	0.15	T;T;T
MetaSVM	Benign	-0.54	T
MutationAssessor	Benign	0.90	L;L;.
PrimateAI	Uncertain	0.51	T
PROVEAN	Benign	-0.17	N;N;N
REVEL	Benign	0.13
Sift	Uncertain	0.0040	D;D;D
Sift4G	Benign	0.50	T;T;T
Polyphen		0.18	B;.;.
Vest4		0.31
MutPred		0.15		Loss of phosphorylation at T21 (P = 0.0123);Loss of phosphorylation at T21 (P = 0.0123);Loss of phosphorylation at T21 (P = 0.0123);
MVP		0.87
MPC		0.37
ClinPred		0.84	D
GERP RS		5.1
Varity_R		0.12
gMVP		0.082

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.030		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: rs376093203; hg19: chr6-30539326;