Genetic Variant ABCF2:c.1338+96C>T (chr7-151217985-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.1338+96C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.102 in 884,042 control chromosomes in the GnomAD database, including 5,284 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 ( 733 hom., cov: 31)

Exomes 𝑓: 0.10 ( 4551 hom. )

Consequence

ABCF2
NM_007189.3 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.342

Publications

18 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:

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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=-0.85).

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.1338+96C>T	intron_variant	Intron 11 of 14	ENST00000287844.7	NP_009120.1	Q9UG63-1A0A090N7X1
ABCF2-H2BK1	NM_005692.5 link	c.1338+96C>T	intron_variant	Intron 11 of 15		NP_005683.2	Q9UG63-2A0A090N7Y2
ABCF2-H2BK1	NR_160983.1 link	n.1423+96C>T	intron_variant	Intron 11 of 16

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein	UniProt
ABCF2	ENST00000287844.7 link	c.1338+96C>T	intron_variant	Intron 11 of 14	1	NM_007189.3	ENSP00000287844.2	Q9UG63-1
ABCF2-H2BK1	ENST00000222388.6 link	c.1338+96C>T	intron_variant	Intron 11 of 15	5		ENSP00000222388.2
ABCF2	ENST00000473874.1 link	n.*175C>T	downstream_gene_variant		3

Frequencies

GnomAD3 genomes

AF:

0.0900

AC:

13663

AN:

151748

Hom.:

732

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0567

Gnomad AMI

AF:

0.0252

Gnomad AMR

AF:

0.0635

Gnomad ASJ

AF:

0.0956

Gnomad EAS

AF:

0.000964

Gnomad SAS

AF:

0.0881

Gnomad FIN

AF:

0.135

Gnomad MID

AF:

0.0728

Gnomad NFE

AF:

0.117

Gnomad OTH

AF:

0.0815

GnomAD4 exome

AF:

0.104

AC:

76385

AN:

732176

Hom.:

4551

AF XY:

0.104

AC XY:

39614

AN XY:

380206

show subpopulations

African (AFR)

AF:

0.0550

AC:

1026

AN:

18662

American (AMR)

AF:

0.0447

AC:

1428

AN:

31978

Ashkenazi Jewish (ASJ)

AF:

0.101

AC:

1695

AN:

16820

East Asian (EAS)

AF:

0.000196

AC:

AN:

35782

South Asian (SAS)

AF:

0.0949

AC:

5625

AN:

59244

European-Finnish (FIN)

AF:

0.142

AC:

6758

AN:

47744

Middle Eastern (MID)

AF:

0.0773

AC:

320

AN:

4140

European-Non Finnish (NFE)

AF:

0.116

AC:

56036

AN:

482232

Other (OTH)

AF:

0.0981

AC:

3490

AN:

35574

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

3244

6488

9731

12975

16219

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

1162

2324

3486

4648

5810

<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:

13665

AN:

151866

Hom.:

733

Cov.:

AF XY:

0.0898

AC XY:

6662

AN XY:

74206

show subpopulations

African (AFR)

AF:

0.0566

AC:

2341

AN:

41378

American (AMR)

AF:

0.0634

AC:

968

AN:

15276

Ashkenazi Jewish (ASJ)

AF:

0.0956

AC:

332

AN:

3472

East Asian (EAS)

AF:

0.000966

AC:

AN:

5174

South Asian (SAS)

AF:

0.0886

AC:

426

AN:

4806

European-Finnish (FIN)

AF:

0.135

AC:

1418

AN:

10508

Middle Eastern (MID)

AF:

0.0714

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.117

AC:

7961

AN:

67938

Other (OTH)

AF:

0.0806

AC:

170

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.494

Heterozygous variant carriers

600

1200

1801

2401

3001

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

166

332

498

664

830

<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:

0.105

Hom.:

309

Bravo

AF:

0.0822

Asia WGS

AF:

0.0410

AC:

143

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.85

CADD

Benign

3.3

(source)

DANN

Benign

0.36

PhyloP100

0.34

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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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