rs1264439

Positions:

• chr6-30584725-A-C

Variant summary

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

The NM_001025091.2(ABCF1):​c.1391+159A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.744 in 151,948 control chromosomes in the GnomAD database, including 42,492 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 0.74 (42492 hom., cov: 31)
• Consequence: ABCF1 NM_001025091.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.737

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=-0.94).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.864 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ABCF1	NM_001025091.2	c.1391+159A>C		intron_variant		ENST00000326195.13
ABCF1	NM_001090.3	c.1277+159A>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ABCF1	ENST00000326195.13	c.1391+159A>C		intron_variant		1	NM_001025091.2	A1
ABCF1	ENST00000376545.7	c.1277+159A>C		intron_variant		1
ABCF1	ENST00000475993.1	c.642+159A>C		intron_variant, NMD_transcript_variant		1
ABCF1	ENST00000441867.6	c.1394+159A>C		intron_variant		5		P3

Frequencies

GnomAD3 genomes AF: 0.744 AC: 112924 AN: 151830 Hom.: 42442 Cov.: 31

Gnomad AFR AF: 0.850

Gnomad AMI AF: 0.754

Gnomad AMR AF: 0.671

Gnomad ASJ AF: 0.846

Gnomad EAS AF: 0.731

Gnomad SAS AF: 0.886

Gnomad FIN AF: 0.684

Gnomad MID AF: 0.823

Gnomad NFE AF: 0.690

Gnomad OTH AF: 0.749

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.744 AC: 113031 AN: 151948 Hom.: 42492 Cov.: 31 AF XY: 0.742 AC XY: 55093 AN XY: 74216

Gnomad4 AFR AF: 0.850

Gnomad4 AMR AF: 0.671

Gnomad4 ASJ AF: 0.846

Gnomad4 EAS AF: 0.730

Gnomad4 SAS AF: 0.886

Gnomad4 FIN AF: 0.684

Gnomad4 NFE AF: 0.690

Gnomad4 OTH AF: 0.751

Alfa AF: 0.710 Hom.: 24338

Bravo AF: 0.747

Asia WGS AF: 0.817 AC: 2842 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.55
DANN	Benign	0.42

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: rs1264439; hg19: chr6-30552502;