rs2537828

Variant names:

• chr17-67646970-T-C
• rs2537828
• NM_012417.4:c.462+14732T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_012417.4(PITPNC1):​c.462+14732T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.859 in 152,234 control chromosomes in the GnomAD database, including 56,499 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 0.86 (56499 hom., cov: 32)
• Consequence: PITPNC1 NM_012417.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.477
• Publications: 7 publications found

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]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.945 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PITPNC1	NM_012417.4	c.462+14732T>C		intron_variant	Intron 6 of 8	ENST00000581322.6	NP_036549.2
PITPNC1	NM_181671.3	c.462+14732T>C		intron_variant	Intron 6 of 9		NP_858057.1
PITPNC1	XM_047435746.1	c.393+14732T>C		intron_variant	Intron 6 of 8		XP_047291702.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PITPNC1	ENST00000581322.6	c.462+14732T>C		intron_variant	Intron 6 of 8	1	NM_012417.4	ENSP00000464006.1
PITPNC1	ENST00000580974.6	c.462+14732T>C		intron_variant	Intron 6 of 9	1		ENSP00000463626.1
PITPNC1	ENST00000578527.1	n.600+14732T>C		intron_variant	Intron 3 of 6	1

Frequencies

GnomAD3 genomes AF: 0.859 AC: 130626 AN: 152116 Hom.: 56431 Cov.: 32

Gnomad AFR AF: 0.952

Gnomad AMI AF: 0.758

Gnomad AMR AF: 0.865

Gnomad ASJ AF: 0.779

Gnomad EAS AF: 0.892

Gnomad SAS AF: 0.811

Gnomad FIN AF: 0.861

Gnomad MID AF: 0.820

Gnomad NFE AF: 0.806

Gnomad OTH AF: 0.862

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.859 AC: 130755 AN: 152234 Hom.: 56499 Cov.: 32 AF XY: 0.860 AC XY: 64028 AN XY: 74430

African (AFR) AF: 0.952 AC: 39572 AN: 41550

American (AMR) AF: 0.865 AC: 13225 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.779 AC: 2701 AN: 3468

East Asian (EAS) AF: 0.892 AC: 4626 AN: 5186

South Asian (SAS) AF: 0.811 AC: 3908 AN: 4820

European-Finnish (FIN) AF: 0.861 AC: 9121 AN: 10596

Middle Eastern (MID) AF: 0.816 AC: 240 AN: 294

European-Non Finnish (NFE) AF: 0.806 AC: 54846 AN: 68008

Other (OTH) AF: 0.863 AC: 1825 AN: 2114

Alfa AF: 0.831 Hom.: 112401

Bravo AF: 0.864

Asia WGS AF: 0.852 AC: 2965 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.1
DANN	Benign	0.49
PhyloP100		-0.48
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs2537828; hg19: chr17-65643086;