dbSNP rs2280934: CHMP7:c.300-58A>G (chr8-23249152-A-G) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_152272.5(CHMP7):c.300-58A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.411 in 1,398,606 control chromosomes in the GnomAD database, including 122,617 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 0.35 ( 10648 hom., cov: 32)

Exomes 𝑓: 0.42 ( 111969 hom. )

Consequence

CHMP7
NM_152272.5 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.110

Publications

11 publications found

Variant links:

Genes affected

CHMP7 (HGNC:28439): (charged multivesicular body protein 7) Involved in several processes, including late endosome to vacuole transport; midbody abscission; and mitotic nuclear division. Located in cytosol; nuclear envelope; and nucleoplasm. Part of ESCRT III complex. Colocalizes with chromatin. [provided by Alliance of Genome Resources, Apr 2022]

CHMP7 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=-0.84).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.501 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_152272.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
CHMP7	NM_152272.5	MANE Select	c.300-58A>G	intron	N/A	NP_689485.1	Q8WUX9-1
CHMP7	NM_001363183.2		c.300-58A>G	intron	N/A	NP_001350112.1
CHMP7	NM_001317899.2		c.-31-58A>G	intron	N/A	NP_001304828.1	B3KRZ9

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
CHMP7	ENST00000397677.6	TSL:1 MANE Select	c.300-58A>G	intron	N/A	ENSP00000380794.1	Q8WUX9-1
CHMP7	ENST00000313219.8	TSL:1	c.300-58A>G	intron	N/A	ENSP00000324491.7	Q8WUX9-1
CHMP7	ENST00000880275.1		c.300-58A>G	intron	N/A	ENSP00000550334.1

Frequencies

GnomAD3 genomes

AF:

0.352

AC:

53473

AN:

151928

Hom.:

10636

Cov.:

show subpopulations

Gnomad AFR

AF:

0.149

Gnomad AMI

AF:

0.408

Gnomad AMR

AF:

0.440

Gnomad ASJ

AF:

0.479

Gnomad EAS

AF:

0.334

Gnomad SAS

AF:

0.519

Gnomad FIN

AF:

0.432

Gnomad MID

AF:

0.449

Gnomad NFE

AF:

0.425

Gnomad OTH

AF:

0.369

GnomAD4 exome

AF:

0.419

AC:

521851

AN:

1246560

Hom.:

111969

AF XY:

0.423

AC XY:

259781

AN XY:

614020

show subpopulations

African (AFR)

AF:

0.139

AC:

3845

AN:

27718

American (AMR)

AF:

0.457

AC:

11696

AN:

25592

Ashkenazi Jewish (ASJ)

AF:

0.469

AC:

8843

AN:

18874

East Asian (EAS)

AF:

0.405

AC:

14750

AN:

36392

South Asian (SAS)

AF:

0.530

AC:

33173

AN:

62570

European-Finnish (FIN)

AF:

0.436

AC:

21278

AN:

48812

Middle Eastern (MID)

AF:

0.474

AC:

1655

AN:

3488

European-Non Finnish (NFE)

AF:

0.417

AC:

405617

AN:

971586

Other (OTH)

AF:

0.407

AC:

20994

AN:

51528

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.508

Heterozygous variant carriers

14203

28406

42609

56812

71015

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

12568

25136

37704

50272

62840

<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:

0.352

AC:

53486

AN:

152046

Hom.:

10648

Cov.:

AF XY:

0.357

AC XY:

26536

AN XY:

74302

show subpopulations

African (AFR)

AF:

0.149

AC:

6192

AN:

41490

American (AMR)

AF:

0.440

AC:

6725

AN:

15270

Ashkenazi Jewish (ASJ)

AF:

0.479

AC:

1663

AN:

3472

East Asian (EAS)

AF:

0.334

AC:

1724

AN:

5164

South Asian (SAS)

AF:

0.518

AC:

2498

AN:

4822

European-Finnish (FIN)

AF:

0.432

AC:

4549

AN:

10542

Middle Eastern (MID)

AF:

0.429

AC:

126

AN:

294

European-Non Finnish (NFE)

AF:

0.425

AC:

28861

AN:

67970

Other (OTH)

AF:

0.368

AC:

777

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

1706

3412

5118

6824

8530

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

532

1064

1596

2128

2660

<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:

0.418

Hom.:

7365

Bravo

AF:

0.339

Asia WGS

AF:

0.406

AC:

1414

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.84

CADD

Benign

1.1

(source)

DANN

Benign

0.51

PhyloP100

-0.11

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