Variant 10-15821734-AAAC-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -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

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:

MINDY3 (HGNC:):

MINDY3 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -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 id 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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MINDY3	NM_024948.4 linkuse as main transcript	c.731-11_731-9delGTT		intron_variant		ENST00000277632.8	NP_079224.1

Ensembl

Gene	Transcript	HGVSc	Effect	TSL	MANE	Protein	UniProt
MINDY3	ENST00000277632.8 linkuse as main transcript	c.731-11_731-9delGTT	intron_variant	1	NM_024948.4	ENSP00000277632.3	Q9H8M7-1
MINDY3	ENST00000477891.1 linkuse as main transcript	n.878-11_878-9delGTT	intron_variant	1
MINDY3	ENST00000418767.5 linkuse as main transcript	c.251-11_251-9delGTT	intron_variant	3		ENSP00000388661.1	X6RC30
MINDY3	ENST00000436829.1 linkuse as main transcript	c.290-11_290-9delGTT	intron_variant	5		ENSP00000389883.1	X6RC97

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

GnomAD3 exomes

AF:

0.00696

AC:

1645

AN:

236336

Hom.:

AF XY:

0.00529

AC XY:

678

AN XY:

128090

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 SAS exome

AF:

0.000964

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

Gnomad4 AFR exome

AF:

0.0712

Gnomad4 AMR exome

AF:

0.00530

Gnomad4 ASJ exome

AF:

0.0186

Gnomad4 EAS exome

AF:

0.000355

Gnomad4 SAS exome

AF:

0.000778

Gnomad4 FIN exome

AF:

0.000455

Gnomad4 NFE exome

AF:

0.000956

Gnomad4 OTH exome

AF:

0.00620

GnomAD4 genome

AF:

0.0210

AC:

3195

AN:

152216

Hom.:

Cov.:

AF XY:

0.0202

AC XY:

1507

AN XY:

74446

show subpopulations

Gnomad4 AFR

AF:

0.0683

Gnomad4 AMR

AF:

0.0107

Gnomad4 ASJ

AF:

0.0179

Gnomad4 EAS

AF:

0.000386

Gnomad4 SAS

AF:

0.00104

Gnomad4 FIN

AF:

0.000283

Gnomad4 NFE

AF:

0.00101

Gnomad4 OTH

AF:

0.0251

Bravo

AF:

0.0246

Asia WGS

AF:

0.00924

AC:

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

Labcorp Genetics (formerly Invitae), Labcorp

Mar 29, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

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

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over