dbSNP rs1122979: 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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_007189.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
ABCF2	NM_007189.3	MANE Select	c.1338+96C>T	intron	N/A	NP_009120.1	A0A090N7X1
ABCF2-H2BK1	NM_005692.5		c.1338+96C>T	intron	N/A	NP_005683.2
ABCF2-H2BK1	NR_160983.1		n.1423+96C>T	intron	N/A

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
ABCF2	ENST00000287844.7	TSL:1 MANE Select	c.1338+96C>T	intron	N/A	ENSP00000287844.2	Q9UG63-1
ABCF2-H2BK1	ENST00000222388.6	TSL:5	c.1338+96C>T	intron	N/A	ENSP00000222388.2
ABCF2	ENST00000889553.1		c.1338+96C>T	intron	N/A	ENSP00000559612.1

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 v4.9

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

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over