rs1318

chr17-67695266-A-Gchr17-67695266-A-T

Variant summary

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

The NM_012417.4(PITPNC1):c.*2378A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.3 in 151,982 control chromosomes in the GnomAD database, including 8,396 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 0.30 (8396 hom., cov: 32)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: PITPNC1 NM_012417.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.48

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]

LOC101928045 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.501 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PITPNC1	NM_012417.4	c.*2378A>G		3_prime_UTR_variant	9/9	ENST00000581322.6
LOC101928045	XR_002958126.2	n.229-5893T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PITPNC1	ENST00000581322.6	c.*2378A>G		3_prime_UTR_variant	9/9	1	NM_012417.4
PITPNC1	ENST00000580974.6	c.*2689A>G		3_prime_UTR_variant	10/10	1		P1

Frequencies

GnomAD3 genomes AF: 0.300 AC: 45495 AN: 151866 Hom.: 8366 Cov.: 32

Gnomad AFR AF: 0.506

Gnomad AMI AF: 0.326

Gnomad AMR AF: 0.224

Gnomad ASJ AF: 0.152

Gnomad EAS AF: 0.479

Gnomad SAS AF: 0.166

Gnomad FIN AF: 0.236

Gnomad MID AF: 0.237

Gnomad NFE AF: 0.205

Gnomad OTH AF: 0.261

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 2 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 2

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.300 AC: 45579 AN: 151982 Hom.: 8396 Cov.: 32 AF XY: 0.298 AC XY: 22143 AN XY: 74292

Gnomad4 AFR AF: 0.506

Gnomad4 AMR AF: 0.224

Gnomad4 ASJ AF: 0.152

Gnomad4 EAS AF: 0.478

Gnomad4 SAS AF: 0.166

Gnomad4 FIN AF: 0.236

Gnomad4 NFE AF: 0.205

Gnomad4 OTH AF: 0.261

Alfa AF: 0.210 Hom.: 5039

Bravo AF: 0.312

Asia WGS AF: 0.308 AC: 1071 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
Cadd	Benign	0.18
Dann	Benign	0.41

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs1318; hg19: chr17-65691382;