6-30573113-C-T

Variant summary

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

The NM_001025091.2(ABCF1):c.73+1553C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.684 in 152,050 control chromosomes in the GnomAD database, including 35,646 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 0.68 (35646 hom., cov: 32)
• Consequence: ABCF1 NM_001025091.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.755

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=-0.8).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.793 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ABCF1	NM_001025091.2	c.73+1553C>T		intron_variant		ENST00000326195.13
ABCF1	NM_001090.3	c.73+1553C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ABCF1	ENST00000326195.13	c.73+1553C>T		intron_variant		1	NM_001025091.2	A1
ABCF1	ENST00000376545.7	c.73+1553C>T		intron_variant		1
ABCF1	ENST00000441867.6	c.73+1553C>T		intron_variant		5		P3
ABCF1	ENST00000468958.1	c.-172+1553C>T		intron_variant		3

Frequencies

GnomAD3 genomes AF: 0.684 AC: 103884 AN: 151930 Hom.: 35615 Cov.: 32

Gnomad AFR AF: 0.731

Gnomad AMI AF: 0.741

Gnomad AMR AF: 0.611

Gnomad ASJ AF: 0.779

Gnomad EAS AF: 0.677

Gnomad SAS AF: 0.814

Gnomad FIN AF: 0.677

Gnomad MID AF: 0.728

Gnomad NFE AF: 0.658

Gnomad OTH AF: 0.666

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

GnomAD4 genome AF: 0.684 AC: 103967 AN: 152050 Hom.: 35646 Cov.: 32 AF XY: 0.683 AC XY: 50770 AN XY: 74322

Gnomad4 AFR AF: 0.731

Gnomad4 AMR AF: 0.612

Gnomad4 ASJ AF: 0.779

Gnomad4 EAS AF: 0.676

Gnomad4 SAS AF: 0.814

Gnomad4 FIN AF: 0.677

Gnomad4 NFE AF: 0.658

Gnomad4 OTH AF: 0.664

Alfa AF: 0.666 Hom.: 45045

Bravo AF: 0.681

Asia WGS AF: 0.734 AC: 2556 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
Cadd	Benign	5.7
Dann	Benign	0.87

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: rs2269709; hg19: chr6-30540890;