Genetic Variant ABCF2:c.723-127C>T (chr7-151222743-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -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

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.60

Publications

44 publications found

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]

ABCF2 links:

ABCF2-H2BK1 (HGNC:54751): (ABCF2-H2BK1 readthrough) This gene represents readthrough transcription between ABCF2 and a downstream histone H2B-like gene. [provided by RefSeq, Mar 2019]

ABCF2-H2BK1 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -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	Effect	Exon rank	MANE	Protein	UniProt
ABCF2	NM_007189.3 link	c.723-127C>T	intron_variant	Intron 5 of 14	ENST00000287844.7	NP_009120.1	Q9UG63-1A0A090N7X1
ABCF2-H2BK1	NM_005692.5 link	c.723-127C>T	intron_variant	Intron 5 of 15		NP_005683.2	Q9UG63-2A0A090N7Y2
ABCF2-H2BK1	NR_160983.1 link	n.808-127C>T	intron_variant	Intron 5 of 16

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein	UniProt
ABCF2	ENST00000287844.7 link	c.723-127C>T	intron_variant	Intron 5 of 14	1	NM_007189.3	ENSP00000287844.2	Q9UG63-1
ABCF2-H2BK1	ENST00000222388.6 link	c.723-127C>T	intron_variant	Intron 5 of 15	5		ENSP00000222388.2
ABCF2	ENST00000468073.5 link	c.723-127C>T	intron_variant	Intron 4 of 5	2		ENSP00000419720.1	C9JZV3

Frequencies

GnomAD3 genomes

AF:

0.0901

AC:

13692

AN:

152010

Hom.:

737

Cov.:

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

African (AFR)

AF:

0.0583

AC:

770

AN:

13214

American (AMR)

AF:

0.0501

AC:

1034

AN:

20652

Ashkenazi Jewish (ASJ)

AF:

0.0997

AC:

1451

AN:

14548

East Asian (EAS)

AF:

0.000199

AC:

AN:

30186

South Asian (SAS)

AF:

0.0955

AC:

4409

AN:

46182

European-Finnish (FIN)

AF:

0.141

AC:

4919

AN:

34844

Middle Eastern (MID)

AF:

0.0788

AC:

282

AN:

3578

European-Non Finnish (NFE)

AF:

0.117

AC:

36706

AN:

314732

Other (OTH)

AF:

0.0979

AC:

2663

AN:

27188

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

2196

4392

6589

8785

10981

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

444

888

1332

1776

2220

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.0900

AC:

13694

AN:

152128

Hom.:

738

Cov.:

AF XY:

0.0898

AC XY:

6676

AN XY:

74362

show subpopulations

African (AFR)

AF:

0.0567

AC:

2352

AN:

41476

American (AMR)

AF:

0.0630

AC:

963

AN:

15278

Ashkenazi Jewish (ASJ)

AF:

0.0956

AC:

332

AN:

3472

East Asian (EAS)

AF:

0.000963

AC:

AN:

5192

South Asian (SAS)

AF:

0.0883

AC:

425

AN:

4814

European-Finnish (FIN)

AF:

0.136

AC:

1435

AN:

10588

Middle Eastern (MID)

AF:

0.0714

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.117

AC:

7968

AN:

67988

Other (OTH)

AF:

0.0804

AC:

170

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

655

1309

1964

2618

3273

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

168

336

504

672

840

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.107

Hom.:

2959

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

(source)

DANN

Benign

0.73

PhyloP100

1.6

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.0

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over