dbSNP rs1046099: MOAP1:c.*31T>C (chr14-93183156-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_022151.5(MOAP1):c.*31T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.683 in 1,564,022 control chromosomes in the GnomAD database, including 366,217 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 0.69 ( 36609 hom., cov: 32)

Exomes 𝑓: 0.68 ( 329608 hom. )

Consequence

MOAP1
NM_022151.5 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.139

Publications

26 publications found

Variant links:

Genes affected

MOAP1 (HGNC:16658): (modulator of apoptosis 1) The protein encoded by this gene was identified by its interaction with apoptosis regulator BAX protein. This protein contains a Bcl-2 homology 3 (BH3)-like motif, which is required for the association with BAX. When overexpressed, this gene has been shown to mediate caspase-dependent apoptosis. [provided by RefSeq, Jul 2008]

MOAP1 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=-0.83).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.744 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MOAP1	NM_022151.5 link	c.*31T>C		3_prime_UTR_variant	Exon 3 of 3	ENST00000298894.5	NP_071434.2	Q96BY2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MOAP1	ENST00000298894.5 link	c.*31T>C		3_prime_UTR_variant	Exon 3 of 3	1	NM_022151.5	ENSP00000298894.4		Q96BY2
MOAP1	ENST00000556883.1 link	c.*31T>C		3_prime_UTR_variant	Exon 2 of 2	2		ENSP00000451594.1		Q96BY2

Frequencies

GnomAD3 genomes

AF:

0.692

AC:

105133

AN:

151950

Hom.:

36582

Cov.:

show subpopulations

Gnomad AFR

AF:

0.751

Gnomad AMI

AF:

0.791

Gnomad AMR

AF:

0.634

Gnomad ASJ

AF:

0.611

Gnomad EAS

AF:

0.693

Gnomad SAS

AF:

0.741

Gnomad FIN

AF:

0.655

Gnomad MID

AF:

0.722

Gnomad NFE

AF:

0.673

Gnomad OTH

AF:

0.708

GnomAD2 exomes

AF:

0.678

AC:

143615

AN:

211968

AF XY:

0.680

show subpopulations

Gnomad AFR exome

AF:

0.752

Gnomad AMR exome

AF:

0.628

Gnomad ASJ exome

AF:

0.608

Gnomad EAS exome

AF:

0.697

Gnomad FIN exome

AF:

0.667

Gnomad NFE exome

AF:

0.672

Gnomad OTH exome

AF:

0.682

GnomAD4 exome

AF:

0.683

AC:

963681

AN:

1411954

Hom.:

329608

Cov.:

AF XY:

0.683

AC XY:

476725

AN XY:

697828

show subpopulations

African (AFR)

AF:

0.757

AC:

24086

AN:

31822

American (AMR)

AF:

0.637

AC:

23995

AN:

37696

Ashkenazi Jewish (ASJ)

AF:

0.606

AC:

13644

AN:

22500

East Asian (EAS)

AF:

0.713

AC:

28066

AN:

39340

South Asian (SAS)

AF:

0.726

AC:

56516

AN:

77826

European-Finnish (FIN)

AF:

0.668

AC:

34231

AN:

51282

Middle Eastern (MID)

AF:

0.715

AC:

3492

AN:

4886

European-Non Finnish (NFE)

AF:

0.680

AC:

739734

AN:

1088442

Other (OTH)

AF:

0.686

AC:

39917

AN:

58160

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.484

Heterozygous variant carriers

16929

33858

50787

67716

84645

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

19372

38744

58116

77488

96860

<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:

0.692

AC:

105216

AN:

152068

Hom.:

36609

Cov.:

AF XY:

0.688

AC XY:

51146

AN XY:

74336

show subpopulations

African (AFR)

AF:

0.751

AC:

31139

AN:

41468

American (AMR)

AF:

0.634

AC:

9690

AN:

15284

Ashkenazi Jewish (ASJ)

AF:

0.611

AC:

2119

AN:

3470

East Asian (EAS)

AF:

0.693

AC:

3586

AN:

5172

South Asian (SAS)

AF:

0.740

AC:

3563

AN:

4816

European-Finnish (FIN)

AF:

0.655

AC:

6926

AN:

10568

Middle Eastern (MID)

AF:

0.714

AC:

210

AN:

294

European-Non Finnish (NFE)

AF:

0.673

AC:

45770

AN:

67978

Other (OTH)

AF:

0.708

AC:

1493

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

1650

3300

4950

6600

8250

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

830

1660

2490

3320

4150

<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:

0.675

Hom.:

60733

Bravo

AF:

0.696

Asia WGS

AF:

0.697

AC:

2425

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.83

CADD

Benign

1.5

(source)

DANN

Benign

0.74

PhyloP100

-0.14

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