rs2017854

chr17-67491905-G-Cchr17-67491905-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_012417.4(PITPNC1):c.49-40897G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.465 in 151,636 control chromosomes in the GnomAD database, including 16,480 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 0.46 (16480 hom., cov: 30)
• Consequence: PITPNC1 NM_012417.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.235

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=-0.76).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.606 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PITPNC1	NM_012417.4	c.49-40897G>C		intron_variant		ENST00000581322.6
PITPNC1	NM_181671.3	c.49-40897G>C		intron_variant
PITPNC1	XM_047435746.1	c.-21-40897G>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PITPNC1	ENST00000581322.6	c.49-40897G>C		intron_variant		1	NM_012417.4
PITPNC1	ENST00000580974.6	c.49-40897G>C		intron_variant		1		P1
PITPNC1	ENST00000584471.5	c.-21-40897G>C		intron_variant		5
PITPNC1	ENST00000584554.1	c.-22+32113G>C		intron_variant		5

Frequencies

GnomAD3 genomes AF: 0.465 AC: 70442 AN: 151514 Hom.: 16474 Cov.: 30

Gnomad AFR AF: 0.422

Gnomad AMI AF: 0.486

Gnomad AMR AF: 0.480

Gnomad ASJ AF: 0.511

Gnomad EAS AF: 0.623

Gnomad SAS AF: 0.484

Gnomad FIN AF: 0.439

Gnomad MID AF: 0.433

Gnomad NFE AF: 0.476

Gnomad OTH AF: 0.442

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

GnomAD4 genome AF: 0.465 AC: 70467 AN: 151636 Hom.: 16480 Cov.: 30 AF XY: 0.462 AC XY: 34237 AN XY: 74074

Gnomad4 AFR AF: 0.422

Gnomad4 AMR AF: 0.479

Gnomad4 ASJ AF: 0.511

Gnomad4 EAS AF: 0.624

Gnomad4 SAS AF: 0.484

Gnomad4 FIN AF: 0.439

Gnomad4 NFE AF: 0.476

Gnomad4 OTH AF: 0.439

Alfa AF: 0.463 Hom.: 2005

Bravo AF: 0.469

Asia WGS AF: 0.505 AC: 1757 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
Cadd	Benign	12
Dann	Benign	0.76

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: rs2017854; hg19: chr17-65488021;