chr17-67491905-G-C

Variant names:

• chr17-67491905-G-C
• rs2017854
• NM_012417.4:c.49-40897G>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.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
• Publications: 12 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=-0.76).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.606 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_012417.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PITPNC1	NM_012417.4	MANE Select	c.49-40897G>C		intron	N/A	NP_036549.2
	PITPNC1	NM_181671.3		c.49-40897G>C		intron	N/A	NP_858057.1	A0A0C4DGP0

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PITPNC1	ENST00000581322.6	TSL:1 MANE Select	c.49-40897G>C		intron	N/A	ENSP00000464006.1	Q9UKF7-1
	PITPNC1	ENST00000580974.6	TSL:1	c.49-40897G>C		intron	N/A	ENSP00000463626.1	A0A0C4DGP0
	PITPNC1	ENST00000584554.1	TSL:5	c.-22+32113G>C		intron	N/A	ENSP00000464364.1	J3QRS7

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

African (AFR) AF: 0.422 AC: 17419 AN: 41298

American (AMR) AF: 0.479 AC: 7304 AN: 15238

Ashkenazi Jewish (ASJ) AF: 0.511 AC: 1770 AN: 3462

East Asian (EAS) AF: 0.624 AC: 3208 AN: 5144

South Asian (SAS) AF: 0.484 AC: 2327 AN: 4810

European-Finnish (FIN) AF: 0.439 AC: 4608 AN: 10494

Middle Eastern (MID) AF: 0.425 AC: 124 AN: 292

European-Non Finnish (NFE) AF: 0.476 AC: 32343 AN: 67886

Other (OTH) AF: 0.439 AC: 923 AN: 2104

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	12
DANN	Benign	0.76
PhyloP100		0.23
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: rs2017854; hg19: chr17-65488021;