17-67695266-A-G

Variant names:

• chr17-67695266-A-G
• rs1318
• NM_012417.4:c.*2378A>G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 10 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=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.501 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PITPNC1	NM_012417.4	MANE Select	c.*2378A>G		3_prime_UTR	Exon 9 of 9	NP_036549.2
	PITPNC1	NM_181671.3		c.*2689A>G		3_prime_UTR	Exon 10 of 10	NP_858057.1
	LOC101928045	NR_188292.1		n.186-5893T>C		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PITPNC1	ENST00000581322.6	TSL:1 MANE Select	c.*2378A>G		3_prime_UTR	Exon 9 of 9	ENSP00000464006.1
	PITPNC1	ENST00000580974.6	TSL:1	c.*2689A>G		3_prime_UTR	Exon 10 of 10	ENSP00000463626.1
	ENSG00000288109	ENST00000832617.1		n.198-5893T>C		intron	N/A

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

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AC: 0 AN: 0

Other (OTH) AF: 0.00 AC: 0 AN: 2

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

African (AFR) AF: 0.506 AC: 20989 AN: 41448

American (AMR) AF: 0.224 AC: 3417 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.152 AC: 526 AN: 3468

East Asian (EAS) AF: 0.478 AC: 2466 AN: 5156

South Asian (SAS) AF: 0.166 AC: 801 AN: 4822

European-Finnish (FIN) AF: 0.236 AC: 2495 AN: 10550

Middle Eastern (MID) AF: 0.245 AC: 72 AN: 294

European-Non Finnish (NFE) AF: 0.205 AC: 13966 AN: 67970

Other (OTH) AF: 0.261 AC: 550 AN: 2104

Alfa AF: 0.238 Hom.: 11593

Bravo AF: 0.312

Asia WGS AF: 0.308 AC: 1071 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.18
DANN	Benign	0.41
PhyloP100		-1.5
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs1318; hg19: chr17-65691382;