rs7812088

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_007189.3(ABCF2):​c.723-127C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.1 in 657,252 control chromosomes in the GnomAD database, including 3,848 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 0.090 ( 738 hom., cov: 32)
Exomes 𝑓: 0.10 ( 3110 hom. )

Consequence

ABCF2
NM_007189.3 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.60
Variant links:
Genes affected
ABCF2 (HGNC:71): (ATP binding cassette subfamily F member 2) This gene encodes a member of the ATP-binding cassette (ABC) transporter superfamily. ATP-binding cassette proteins transport various molecules across extra- and intracellular membranes. Alterations in this gene may be involved in cancer progression. Related pseudogenes have been identified on chromosomes 3 and 7. [provided by RefSeq, Mar 2019]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.79).
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
ABCF2NM_007189.3 linkuse as main transcriptc.723-127C>T intron_variant ENST00000287844.7 NP_009120.1
ABCF2-H2BK1NR_160983.1 linkuse as main transcriptn.808-127C>T intron_variant, non_coding_transcript_variant
ABCF2-H2BK1NM_005692.5 linkuse as main transcriptc.723-127C>T intron_variant NP_005683.2

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
ABCF2ENST00000287844.7 linkuse as main transcriptc.723-127C>T intron_variant 1 NM_007189.3 ENSP00000287844 P1Q9UG63-1
ABCF2ENST00000468073.5 linkuse as main transcriptc.723-127C>T intron_variant 2 ENSP00000419720

Frequencies

GnomAD3 genomes
AF:
0.0901
AC:
13692
AN:
152010
Hom.:
737
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0568
Gnomad AMI
AF:
0.0252
Gnomad AMR
AF:
0.0631
Gnomad ASJ
AF:
0.0956
Gnomad EAS
AF:
0.000961
Gnomad SAS
AF:
0.0878
Gnomad FIN
AF:
0.136
Gnomad MID
AF:
0.0728
Gnomad NFE
AF:
0.117
Gnomad OTH
AF:
0.0813
GnomAD4 exome
AF:
0.103
AC:
52240
AN:
505124
Hom.:
3110
AF XY:
0.103
AC XY:
27462
AN XY:
266230
show subpopulations
Gnomad4 AFR exome
AF:
0.0583
Gnomad4 AMR exome
AF:
0.0501
Gnomad4 ASJ exome
AF:
0.0997
Gnomad4 EAS exome
AF:
0.000199
Gnomad4 SAS exome
AF:
0.0955
Gnomad4 FIN exome
AF:
0.141
Gnomad4 NFE exome
AF:
0.117
Gnomad4 OTH exome
AF:
0.0979
GnomAD4 genome
AF:
0.0900
AC:
13694
AN:
152128
Hom.:
738
Cov.:
32
AF XY:
0.0898
AC XY:
6676
AN XY:
74362
show subpopulations
Gnomad4 AFR
AF:
0.0567
Gnomad4 AMR
AF:
0.0630
Gnomad4 ASJ
AF:
0.0956
Gnomad4 EAS
AF:
0.000963
Gnomad4 SAS
AF:
0.0883
Gnomad4 FIN
AF:
0.136
Gnomad4 NFE
AF:
0.117
Gnomad4 OTH
AF:
0.0804
Alfa
AF:
0.105
Hom.:
1081
Bravo
AF:
0.0822
Asia WGS
AF:
0.0410
AC:
142
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.79
CADD
Benign
12
DANN
Benign
0.73
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.0

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.050
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

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs7812088; hg19: chr7-150919829; COSMIC: COSV55182533; COSMIC: COSV55182533; API