rs1264440

chr6-30583509-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001025091.2(ABCF1):c.916-99A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.689 in 1,276,494 control chromosomes in the GnomAD database, including 305,328 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 0.69 (36513 hom., cov: 31)
  • Exomes 𝑓: 0.69 (268815 hom.)
• Consequence: ABCF1 NM_001025091.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.18

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 Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.71).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.832 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ABCF1	NM_001025091.2	c.916-99A>G		intron_variant		ENST00000326195.13
ABCF1	NM_001090.3	c.802-99A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ABCF1	ENST00000326195.13	c.916-99A>G		intron_variant		1	NM_001025091.2	A1
ABCF1	ENST00000376545.7	c.802-99A>G		intron_variant		1
ABCF1	ENST00000475993.1	c.167-99A>G		intron_variant, NMD_transcript_variant		1
ABCF1	ENST00000441867.6	c.919-99A>G		intron_variant		5		P3

Frequencies

GnomAD3 genomes AF: 0.692 AC: 105043 AN: 151852 Hom.: 36478 Cov.: 31

Gnomad AFR AF: 0.737

Gnomad AMI AF: 0.743

Gnomad AMR AF: 0.621

Gnomad ASJ AF: 0.788

Gnomad EAS AF: 0.679

Gnomad SAS AF: 0.853

Gnomad FIN AF: 0.677

Gnomad MID AF: 0.722

Gnomad NFE AF: 0.666

Gnomad OTH AF: 0.679

GnomAD4 exome AF: 0.689 AC: 774250 AN: 1124524 Hom.: 268815 AF XY: 0.695 AC XY: 395207 AN XY: 568752

Gnomad4 AFR exome AF: 0.749

Gnomad4 AMR exome AF: 0.640

Gnomad4 ASJ exome AF: 0.787

Gnomad4 EAS exome AF: 0.683

Gnomad4 SAS exome AF: 0.843

Gnomad4 FIN exome AF: 0.672

Gnomad4 NFE exome AF: 0.672

Gnomad4 OTH exome AF: 0.705

GnomAD4 genome AF: 0.692 AC: 105131 AN: 151970 Hom.: 36513 Cov.: 31 AF XY: 0.691 AC XY: 51359 AN XY: 74274

Gnomad4 AFR AF: 0.738

Gnomad4 AMR AF: 0.621

Gnomad4 ASJ AF: 0.788

Gnomad4 EAS AF: 0.678

Gnomad4 SAS AF: 0.853

Gnomad4 FIN AF: 0.677

Gnomad4 NFE AF: 0.666

Gnomad4 OTH AF: 0.678

Alfa AF: 0.681 Hom.: 60532

Bravo AF: 0.689

Asia WGS AF: 0.747 AC: 2600 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.71
Cadd	Benign	7.4
Dann	Benign	0.86

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: rs1264440; hg19: chr6-30551286; COSMIC: COSV58229016; COSMIC: COSV58229016;