rs2537828

chr17-67646970-T-C

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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/exons	MANE	UniProt
PITPNC1	NM_012417.4	c.462+14732T>C		intron_variant		ENST00000581322.6
PITPNC1	NM_181671.3	c.462+14732T>C		intron_variant
PITPNC1	XM_047435746.1	c.393+14732T>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PITPNC1	ENST00000581322.6	c.462+14732T>C		intron_variant		1	NM_012417.4
PITPNC1	ENST00000580974.6	c.462+14732T>C		intron_variant		1		P1
PITPNC1	ENST00000578527.1	n.600+14732T>C		intron_variant, non_coding_transcript_variant		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

Gnomad4 AFR AF: 0.952

Gnomad4 AMR AF: 0.865

Gnomad4 ASJ AF: 0.779

Gnomad4 EAS AF: 0.892

Gnomad4 SAS AF: 0.811

Gnomad4 FIN AF: 0.861

Gnomad4 NFE AF: 0.806

Gnomad4 OTH AF: 0.863

Alfa AF: 0.824 Hom.: 22555

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

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

Other links and lift over

dbSNP: rs2537828; hg19: chr17-65643086;