17-67680693-C-T

Variant names:

• chr17-67680693-C-T
• rs2625563
• NM_012417.4:c.682+5151C>T

Variant summary

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

The NM_012417.4(PITPNC1):​c.682+5151C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.833 in 152,146 control chromosomes in the GnomAD database, including 52,843 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 0.83 (52843 hom., cov: 31)
• Consequence: PITPNC1 NM_012417.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0290
• Publications: 5 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]

ENSG00000288109 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.849 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PITPNC1	NM_012417.4	c.682+5151C>T		intron_variant	Intron 8 of 8	ENST00000581322.6	NP_036549.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PITPNC1	ENST00000581322.6	c.682+5151C>T		intron_variant	Intron 8 of 8	1	NM_012417.4	ENSP00000464006.1

Frequencies

GnomAD3 genomes AF: 0.833 AC: 126621 AN: 152028 Hom.: 52786 Cov.: 31

Gnomad AFR AF: 0.821

Gnomad AMI AF: 0.765

Gnomad AMR AF: 0.861

Gnomad ASJ AF: 0.793

Gnomad EAS AF: 0.865

Gnomad SAS AF: 0.810

Gnomad FIN AF: 0.865

Gnomad MID AF: 0.845

Gnomad NFE AF: 0.830

Gnomad OTH AF: 0.849

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

GnomAD4 genome AF: 0.833 AC: 126739 AN: 152146 Hom.: 52843 Cov.: 31 AF XY: 0.835 AC XY: 62071 AN XY: 74374

African (AFR) AF: 0.821 AC: 34070 AN: 41486

American (AMR) AF: 0.862 AC: 13179 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.793 AC: 2752 AN: 3470

East Asian (EAS) AF: 0.865 AC: 4473 AN: 5172

South Asian (SAS) AF: 0.810 AC: 3908 AN: 4824

European-Finnish (FIN) AF: 0.865 AC: 9150 AN: 10576

Middle Eastern (MID) AF: 0.840 AC: 247 AN: 294

European-Non Finnish (NFE) AF: 0.830 AC: 56472 AN: 68014

Other (OTH) AF: 0.851 AC: 1790 AN: 2104

Alfa AF: 0.832 Hom.: 96972

Bravo AF: 0.833

Asia WGS AF: 0.835 AC: 2899 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.5
DANN	Benign	0.66
PhyloP100		0.029
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: rs2625563; hg19: chr17-65676809;