6-30573460-G-T

Variant names:

• chr6-30573460-G-T
• rs1264451
• NM_001025091.2:c.73+1900G>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001025091.2(ABCF1):​c.73+1900G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.741 in 152,124 control chromosomes in the GnomAD database, including 42,190 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 (42190 hom., cov: 32)
• Consequence: ABCF1 NM_001025091.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.571
• Publications: 11 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=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.842 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ABCF1	NM_001025091.2	c.73+1900G>T		intron_variant	Intron 1 of 24	ENST00000326195.13	NP_001020262.1
ABCF1	NM_001090.3	c.73+1900G>T		intron_variant	Intron 1 of 23		NP_001081.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ABCF1	ENST00000326195.13	c.73+1900G>T		intron_variant	Intron 1 of 24	1	NM_001025091.2	ENSP00000313603.8
ABCF1	ENST00000376545.7	c.73+1900G>T		intron_variant	Intron 1 of 23	1		ENSP00000365728.3
ABCF1	ENST00000441867.6	c.73+1900G>T		intron_variant	Intron 1 of 24	5		ENSP00000405512.2
ABCF1	ENST00000468958.1	c.-172+1900G>T		intron_variant	Intron 1 of 6	3		ENSP00000440893.1

Frequencies

GnomAD3 genomes AF: 0.741 AC: 112628 AN: 152006 Hom.: 42140 Cov.: 32

Gnomad AFR AF: 0.849

Gnomad AMI AF: 0.753

Gnomad AMR AF: 0.669

Gnomad ASJ AF: 0.846

Gnomad EAS AF: 0.727

Gnomad SAS AF: 0.840

Gnomad FIN AF: 0.684

Gnomad MID AF: 0.820

Gnomad NFE AF: 0.688

Gnomad OTH AF: 0.747

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

GnomAD4 genome AF: 0.741 AC: 112734 AN: 152124 Hom.: 42190 Cov.: 32 AF XY: 0.738 AC XY: 54910 AN XY: 74366

African (AFR) AF: 0.849 AC: 35249 AN: 41500

American (AMR) AF: 0.669 AC: 10217 AN: 15268

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

East Asian (EAS) AF: 0.726 AC: 3759 AN: 5180

South Asian (SAS) AF: 0.840 AC: 4060 AN: 4832

European-Finnish (FIN) AF: 0.684 AC: 7239 AN: 10580

Middle Eastern (MID) AF: 0.813 AC: 239 AN: 294

European-Non Finnish (NFE) AF: 0.688 AC: 46765 AN: 67972

Other (OTH) AF: 0.749 AC: 1585 AN: 2116

Alfa AF: 0.734 Hom.: 28118

Bravo AF: 0.746

Asia WGS AF: 0.798 AC: 2775 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.38
DANN	Benign	0.48
PhyloP100		-0.57
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: rs1264451; hg19: chr6-30541237;