17-67680693-C-T

Position:

• chr17-67680693-C-T

Variant summary

Our verdict is Benign. Variant got -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

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]

PITPNC1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
PITPNC1	NM_012417.4	c.682+5151C>T		intron_variant		ENST00000581322.6	NP_036549.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PITPNC1	ENST00000581322.6	c.682+5151C>T		intron_variant		1	NM_012417.4	ENSP00000464006.1
PITPNC1	ENST00000580974.6	c.682+5151C>T		intron_variant		1		ENSP00000463626.1
PITPNC1	ENST00000578527.1	n.820+5151C>T		intron_variant		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

Gnomad4 AFR AF: 0.821

Gnomad4 AMR AF: 0.862

Gnomad4 ASJ AF: 0.793

Gnomad4 EAS AF: 0.865

Gnomad4 SAS AF: 0.810

Gnomad4 FIN AF: 0.865

Gnomad4 NFE AF: 0.830

Gnomad4 OTH AF: 0.851

Alfa AF: 0.831 Hom.: 69623

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

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: rs2625563; hg19: chr17-65676809;