Genetic Variant MINDY3:c.731-11_731-9delGTT (chr10-15821734-AAAC-A) – ACMG Classification: Benign (-10 pts)

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP6_ModerateBA1

The NM_024948.4(MINDY3):c.731-11_731-9delGTT variant causes a intron change. The variant allele was found at a frequency of 0.00487 in 1,606,218 control chromosomes in the GnomAD database, including 194 homozygotes. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.021 ( 98 hom., cov: 32)

Exomes 𝑓: 0.0032 ( 96 hom. )

Consequence

MINDY3
NM_024948.4 intron

Scores

Not classified

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 3.87

Publications

0 publications found

Variant links:

Genes affected

MINDY3 (HGNC:23578): (MINDY lysine 48 deubiquitinase 3) The protein encoded by this gene contains a caspase-associated recruitment domain and may function in apoptosis. It has been identified as a tumor suppressor in lung and gastric cancers, and a polymorphism in the gene may be associated with gastric cancer risk. Alternative splicing of this gene results in multiple transcript variants. [provided by RefSeq, Dec 2015]

MINDY3 links:

LOC124902383 (HGNC:):

LOC124902383 links:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -10 ACMG points.

BP6

Variant 10-15821734-AAAC-A is Benign according to our data. Variant chr10-15821734-AAAC-A is described in ClinVar as Benign. ClinVar VariationId is 711900.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0662 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_024948.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MINDY3	NM_024948.4	MANE Select	c.731-11_731-9delGTT		intron	N/A	NP_079224.1	Q9H8M7-1
	MINDY3	NM_001318330.2		c.212-11_212-9delGTT		intron	N/A	NP_001305259.1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
MINDY3	ENST00000277632.8	TSL:1 MANE Select	c.731-11_731-9delGTT	intron	N/A	ENSP00000277632.3	Q9H8M7-1
MINDY3	ENST00000477891.1	TSL:1	n.878-11_878-9delGTT	intron	N/A
MINDY3	ENST00000953409.1		c.731-11_731-9delGTT	intron	N/A	ENSP00000623468.1

Frequencies

GnomAD3 genomes

AF:

0.0209

AC:

3185

AN:

152100

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0682

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0108

Gnomad ASJ

AF:

0.0179

Gnomad EAS

AF:

0.000385

Gnomad SAS

AF:

0.00104

Gnomad FIN

AF:

0.000283

Gnomad MID

AF:

0.00949

Gnomad NFE

AF:

0.00101

Gnomad OTH

AF:

0.0253

GnomAD2 exomes

AF:

0.00696

AC:

1645

AN:

236336

AF XY:

0.00529

show subpopulations

Gnomad AFR exome

AF:

0.0714

Gnomad AMR exome

AF:

0.00465

Gnomad ASJ exome

AF:

0.0193

Gnomad EAS exome

AF:

0.000350

Gnomad FIN exome

AF:

0.000728

Gnomad NFE exome

AF:

0.00117

Gnomad OTH exome

AF:

0.00474

GnomAD4 exome

AF:

0.00319

AC:

4635

AN:

1454002

Hom.:

AF XY:

0.00295

AC XY:

2133

AN XY:

723332

show subpopulations

African (AFR)

AF:

0.0712

AC:

2344

AN:

32910

American (AMR)

AF:

0.00530

AC:

231

AN:

43614

Ashkenazi Jewish (ASJ)

AF:

0.0186

AC:

481

AN:

25916

East Asian (EAS)

AF:

0.000355

AC:

AN:

39490

South Asian (SAS)

AF:

0.000778

AC:

AN:

84808

European-Finnish (FIN)

AF:

0.000455

AC:

AN:

52796

Middle Eastern (MID)

AF:

0.00750

AC:

AN:

5730

European-Non Finnish (NFE)

AF:

0.000956

AC:

1060

AN:

1108716

Other (OTH)

AF:

0.00620

AC:

372

AN:

60022

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.499

Heterozygous variant carriers

221

442

662

883

1104

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

102

204

306

408

510

<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:

0.0210

AC:

3195

AN:

152216

Hom.:

Cov.:

AF XY:

0.0202

AC XY:

1507

AN XY:

74446

show subpopulations

African (AFR)

AF:

0.0683

AC:

2834

AN:

41520

American (AMR)

AF:

0.0107

AC:

164

AN:

15282

Ashkenazi Jewish (ASJ)

AF:

0.0179

AC:

AN:

3470

East Asian (EAS)

AF:

0.000386

AC:

AN:

5186

South Asian (SAS)

AF:

0.00104

AC:

AN:

4822

European-Finnish (FIN)

AF:

0.000283

AC:

AN:

10608

Middle Eastern (MID)

AF:

0.0102

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.00101

AC:

AN:

68008

Other (OTH)

AF:

0.0251

AC:

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.494

Heterozygous variant carriers

145

290

435

580

725

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

128

160

<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:

0.00538

Hom.:

Bravo

AF:

0.0246

Asia WGS

AF:

0.00924

AC:

AN:

3478

ClinVar

ClinVar submissions

Significance:Benign

Revision:criteria provided, single submitter

View on ClinVar

Pathogenic

VUS

Benign

Condition

not provided (1)

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

PhyloP100

3.9

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

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