Genetic Variant PITPNC1:c.-292C>G (chr17-67377863-C-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_012417.4(PITPNC1):c.-292C>G variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.315 in 362,564 control chromosomes in the GnomAD database, including 20,455 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 0.27 ( 6956 hom., cov: 32)

Exomes 𝑓: 0.35 ( 13499 hom. )

Consequence

PITPNC1
NM_012417.4 5_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0890

Publications

8 publications found

Variant links:

Genes affected

PITPNC1 (HGNC:21045): (phosphatidylinositol transfer protein cytoplasmic 1) This gene encodes a member of the phosphatidylinositol transfer protein family. The encoded cytoplasmic protein plays a role in multiple processes including cell signaling and lipid metabolism by facilitating the transfer of phosphatidylinositol between membrane compartments. Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene, and a pseudogene of this gene is located on the long arm of chromosome 1. [provided by RefSeq, May 2012]

PITPNC1 links:

ENSG00000297739 (HGNC:):

ENSG00000297739 links:

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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=-0.85).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.376 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PITPNC1	NM_012417.4 link	c.-292C>G		5_prime_UTR_variant	Exon 1 of 9	ENST00000581322.6	NP_036549.2	Q9UKF7-1
PITPNC1	NM_181671.3 link	c.-292C>G		5_prime_UTR_variant	Exon 1 of 10		NP_858057.1	Q9UKF7A0A0C4DGP0

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein	UniProt
PITPNC1	ENST00000581322.6 link	c.-292C>G	5_prime_UTR_variant	Exon 1 of 9	1	NM_012417.4	ENSP00000464006.1	Q9UKF7-1
PITPNC1	ENST00000580974.6 link	c.-292C>G	5_prime_UTR_variant	Exon 1 of 10	1		ENSP00000463626.1	A0A0C4DGP0
ENSG00000297739	ENST00000750645.1 link	n.43G>C	non_coding_transcript_exon_variant	Exon 1 of 2

Frequencies

GnomAD3 genomes

AF:

0.270

AC:

41112

AN:

152044

Hom.:

6959

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0728

Gnomad AMI

AF:

0.337

Gnomad AMR

AF:

0.259

Gnomad ASJ

AF:

0.231

Gnomad EAS

AF:

0.323

Gnomad SAS

AF:

0.218

Gnomad FIN

AF:

0.368

Gnomad MID

AF:

0.171

Gnomad NFE

AF:

0.380

Gnomad OTH

AF:

0.268

GnomAD4 exome

AF:

0.347

AC:

72961

AN:

210402

Hom.:

13499

Cov.:

AF XY:

0.346

AC XY:

36973

AN XY:

106968

show subpopulations

African (AFR)

AF:

0.0718

AC:

395

AN:

5498

American (AMR)

AF:

0.273

AC:

1488

AN:

5448

Ashkenazi Jewish (ASJ)

AF:

0.231

AC:

1701

AN:

7364

East Asian (EAS)

AF:

0.360

AC:

6184

AN:

17200

South Asian (SAS)

AF:

0.196

AC:

1218

AN:

6200

European-Finnish (FIN)

AF:

0.373

AC:

6831

AN:

18296

Middle Eastern (MID)

AF:

0.167

AC:

182

AN:

1092

European-Non Finnish (NFE)

AF:

0.374

AC:

50636

AN:

135378

Other (OTH)

AF:

0.311

AC:

4326

AN:

13926

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.506

Heterozygous variant carriers

2157

4314

6471

8628

10785

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

200

400

600

800

1000

<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:

0.270

AC:

41114

AN:

152162

Hom.:

6956

Cov.:

AF XY:

0.269

AC XY:

20010

AN XY:

74398

show subpopulations

African (AFR)

AF:

0.0727

AC:

3021

AN:

41564

American (AMR)

AF:

0.260

AC:

3969

AN:

15294

Ashkenazi Jewish (ASJ)

AF:

0.231

AC:

802

AN:

3470

East Asian (EAS)

AF:

0.323

AC:

1667

AN:

5160

South Asian (SAS)

AF:

0.219

AC:

1057

AN:

4826

European-Finnish (FIN)

AF:

0.368

AC:

3899

AN:

10594

Middle Eastern (MID)

AF:

0.160

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.380

AC:

25786

AN:

67938

Other (OTH)

AF:

0.265

AC:

560

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1444

2889

4333

5778

7222

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

422

844

1266

1688

2110

<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:

0.228

Hom.:

674

Bravo

AF:

0.255

Asia WGS

AF:

0.247

AC:

858

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.85

CADD

Benign

7.9

(source)

DANN

Benign

0.82

PhyloP100

-0.089

PromoterAI

-0.21

Neutral

(source)

Mutation Taster

=300/0

polymorphism (auto)

(source)

Splicing

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