6-30583509-A-G

Variant names:

• chr6-30583509-A-G
• rs1264440
• NM_001025091.2:c.916-99A>G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 29 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=-0.71).
• 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 rank	MANE	Protein	UniProt
ABCF1	NM_001025091.2	c.916-99A>G		intron_variant	Intron 10 of 24	ENST00000326195.13	NP_001020262.1
ABCF1	NM_001090.3	c.802-99A>G		intron_variant	Intron 9 of 23		NP_001081.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ABCF1	ENST00000326195.13	c.916-99A>G		intron_variant	Intron 10 of 24	1	NM_001025091.2	ENSP00000313603.8
ABCF1	ENST00000376545.7	c.802-99A>G		intron_variant	Intron 9 of 23	1		ENSP00000365728.3
ABCF1	ENST00000475993.1	n.166-99A>G		intron_variant	Intron 2 of 17	1		ENSP00000445100.1
ABCF1	ENST00000441867.6	c.919-99A>G		intron_variant	Intron 10 of 24	5		ENSP00000405512.2

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

African (AFR) AF: 0.749 AC: 20036 AN: 26738

American (AMR) AF: 0.640 AC: 26437 AN: 41318

Ashkenazi Jewish (ASJ) AF: 0.787 AC: 17091 AN: 21726

East Asian (EAS) AF: 0.683 AC: 25912 AN: 37924

South Asian (SAS) AF: 0.843 AC: 62903 AN: 74626

European-Finnish (FIN) AF: 0.672 AC: 33560 AN: 49924

Middle Eastern (MID) AF: 0.756 AC: 3066 AN: 4058

European-Non Finnish (NFE) AF: 0.672 AC: 550920 AN: 819518

Other (OTH) AF: 0.705 AC: 34325 AN: 48692

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

African (AFR) AF: 0.738 AC: 30567 AN: 41446

American (AMR) AF: 0.621 AC: 9479 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.788 AC: 2727 AN: 3462

East Asian (EAS) AF: 0.678 AC: 3499 AN: 5158

South Asian (SAS) AF: 0.853 AC: 4117 AN: 4824

European-Finnish (FIN) AF: 0.677 AC: 7149 AN: 10560

Middle Eastern (MID) AF: 0.711 AC: 209 AN: 294

European-Non Finnish (NFE) AF: 0.666 AC: 45281 AN: 67944

Other (OTH) AF: 0.678 AC: 1431 AN: 2112

Alfa AF: 0.679 Hom.: 135395

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
PhyloP100		-1.2
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: rs1264440; hg19: chr6-30551286; COSMIC: COSV58229016; COSMIC: COSV58229016;