6-30584725-A-C

Variant names:

• chr6-30584725-A-C
• rs1264439
• NM_001025091.2:c.1391+159A>C

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 18 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: Benign. The variant received -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 rank	MANE	Protein	UniProt
ABCF1	NM_001025091.2	c.1391+159A>C		intron_variant	Intron 14 of 24	ENST00000326195.13	NP_001020262.1
ABCF1	NM_001090.3	c.1277+159A>C		intron_variant	Intron 13 of 23		NP_001081.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ABCF1	ENST00000326195.13	c.1391+159A>C		intron_variant	Intron 14 of 24	1	NM_001025091.2	ENSP00000313603.8
ABCF1	ENST00000376545.7	c.1277+159A>C		intron_variant	Intron 13 of 23	1		ENSP00000365728.3
ABCF1	ENST00000475993.1	n.641+159A>C		intron_variant	Intron 6 of 17	1		ENSP00000445100.1
ABCF1	ENST00000441867.6	c.1394+159A>C		intron_variant	Intron 14 of 24	5		ENSP00000405512.2

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

African (AFR) AF: 0.850 AC: 35274 AN: 41494

American (AMR) AF: 0.671 AC: 10226 AN: 15240

Ashkenazi Jewish (ASJ) AF: 0.846 AC: 2936 AN: 3472

East Asian (EAS) AF: 0.730 AC: 3753 AN: 5140

South Asian (SAS) AF: 0.886 AC: 4272 AN: 4822

European-Finnish (FIN) AF: 0.684 AC: 7210 AN: 10538

Middle Eastern (MID) AF: 0.816 AC: 240 AN: 294

European-Non Finnish (NFE) AF: 0.690 AC: 46847 AN: 67926

Other (OTH) AF: 0.751 AC: 1587 AN: 2112

Alfa AF: 0.713 Hom.: 98552

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
PhyloP100		-0.74
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs1264439; hg19: chr6-30552502;