rs3132610

Positions:

• chr6-30576624-A-G

Variant summary

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

The NM_001025091.2(ABCF1):​c.74-785A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0722 in 151,670 control chromosomes in the GnomAD database, including 593 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 0.072 (593 hom., cov: 30)
• Consequence: ABCF1 NM_001025091.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.528

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=-0.99).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.115 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ABCF1	NM_001025091.2	c.74-785A>G		intron_variant		ENST00000326195.13	NP_001020262.1
ABCF1	NM_001090.3	c.74-785A>G		intron_variant			NP_001081.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ABCF1	ENST00000326195.13	c.74-785A>G		intron_variant		1	NM_001025091.2	ENSP00000313603	A1
ABCF1	ENST00000376545.7	c.74-785A>G		intron_variant		1		ENSP00000365728
ABCF1	ENST00000441867.6	c.74-785A>G		intron_variant		5		ENSP00000405512	P3
ABCF1	ENST00000468958.1	c.-171-1194A>G		intron_variant		3		ENSP00000440893

Frequencies

GnomAD3 genomes AF: 0.0723 AC: 10959 AN: 151552 Hom.: 593 Cov.: 30

Gnomad AFR AF: 0.0345

Gnomad AMI AF: 0.148

Gnomad AMR AF: 0.0323

Gnomad ASJ AF: 0.0314

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.000417

Gnomad FIN AF: 0.0693

Gnomad MID AF: 0.00633

Gnomad NFE AF: 0.117

Gnomad OTH AF: 0.0519

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

GnomAD4 genome AF: 0.0722 AC: 10958 AN: 151670 Hom.: 593 Cov.: 30 AF XY: 0.0657 AC XY: 4874 AN XY: 74134

Gnomad4 AFR AF: 0.0345

Gnomad4 AMR AF: 0.0321

Gnomad4 ASJ AF: 0.0314

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.000209

Gnomad4 FIN AF: 0.0693

Gnomad4 NFE AF: 0.117

Gnomad4 OTH AF: 0.0514

Alfa AF: 0.102 Hom.: 1752

Bravo AF: 0.0686

Asia WGS AF: 0.00577 AC: 21 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	2.2
DANN	Benign	0.33

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: rs3132610; hg19: chr6-30544401;