Genetic Variant PITPNM2:c.*927C>A (chr12-122985100-G-T) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The NM_020845.3(PITPNM2):c.*927C>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.541 in 152,482 control chromosomes in the GnomAD database, including 26,935 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 0.54 ( 26843 hom., cov: 33)

Exomes 𝑓: 0.74 ( 92 hom. )

Consequence

PITPNM2
NM_020845.3 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 2.17

Publications

15 publications found

Variant links:

Genes affected

PITPNM2 (HGNC:21044): (phosphatidylinositol transfer protein membrane associated 2) PITPNM2 belongs to a family of membrane-associated phosphatidylinositol transfer domain-containing proteins that share homology with the Drosophila retinal degeneration B (rdgB) protein (Ocaka et al., 2005 [PubMed 15627748]).[supplied by OMIM, Mar 2008]

PITPNM2 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=-0.57).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.702 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_020845.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
PITPNM2	NM_020845.3	MANE Select	c.*927C>A	3_prime_UTR	Exon 26 of 26	NP_065896.1	Q9BZ72-1
PITPNM2	NM_001384660.1		c.*927C>A	3_prime_UTR	Exon 26 of 26	NP_001371589.1
PITPNM2	NM_001300801.2		c.*927C>A	3_prime_UTR	Exon 26 of 26	NP_001287730.1	Q9BZ72-2

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
PITPNM2	ENST00000320201.10	TSL:5 MANE Select	c.*927C>A	3_prime_UTR	Exon 26 of 26	ENSP00000322218.4	Q9BZ72-1
PITPNM2	ENST00000876870.1		c.*927C>A	3_prime_UTR	Exon 25 of 25	ENSP00000546929.1
PITPNM2	ENST00000280562.9	TSL:5	c.*927C>A	3_prime_UTR	Exon 25 of 25	ENSP00000280562.5	Q9BZ72-2

Frequencies

GnomAD3 genomes

AF:

0.541

AC:

82172

AN:

152020

Hom.:

26849

Cov.:

show subpopulations

Gnomad AFR

AF:

0.151

Gnomad AMI

AF:

0.747

Gnomad AMR

AF:

0.638

Gnomad ASJ

AF:

0.619

Gnomad EAS

AF:

0.673

Gnomad SAS

AF:

0.575

Gnomad FIN

AF:

0.718

Gnomad MID

AF:

0.560

Gnomad NFE

AF:

0.707

Gnomad OTH

AF:

0.578

GnomAD4 exome

AF:

0.735

AC:

253

AN:

344

Hom.:

Cov.:

AF XY:

0.735

AC XY:

144

AN XY:

196

show subpopulations

African (AFR)

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AF:

0.744

AC:

247

AN:

332

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.625

AC:

AN:

Other (OTH)

AF:

0.500

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.522

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

<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:

0.540

AC:

82165

AN:

152138

Hom.:

26843

Cov.:

AF XY:

0.544

AC XY:

40456

AN XY:

74376

show subpopulations

African (AFR)

AF:

0.151

AC:

6271

AN:

41516

American (AMR)

AF:

0.637

AC:

9740

AN:

15288

Ashkenazi Jewish (ASJ)

AF:

0.619

AC:

2148

AN:

3468

East Asian (EAS)

AF:

0.673

AC:

3482

AN:

5176

South Asian (SAS)

AF:

0.577

AC:

2781

AN:

4822

European-Finnish (FIN)

AF:

0.718

AC:

7586

AN:

10566

Middle Eastern (MID)

AF:

0.568

AC:

167

AN:

294

European-Non Finnish (NFE)

AF:

0.707

AC:

48094

AN:

67986

Other (OTH)

AF:

0.576

AC:

1215

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1490

2981

4471

5962

7452

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

686

1372

2058

2744

3430

<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:

0.479

Hom.:

2433

Bravo

AF:

0.513

Asia WGS

AF:

0.563

AC:

1958

AN:

3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.57

CADD

Benign

(source)

DANN

Benign

0.81

PhyloP100

2.2

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.030

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