17-67584155-T-C

Variant names:

• chr17-67584155-T-C
• rs2570054
• NM_012417.4:c.366+5898T>C

Variant summary

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

The NM_012417.4(PITPNC1):​c.366+5898T>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 151,788 control chromosomes in the GnomAD database, including 16,696 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 0.47 (16696 hom., cov: 30)
• Consequence: PITPNC1 NM_012417.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0550

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.612 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PITPNC1	NM_012417.4	c.366+5898T>C		intron_variant	Intron 5 of 8	ENST00000581322.6	NP_036549.2
PITPNC1	NM_181671.3	c.366+5898T>C		intron_variant	Intron 5 of 9		NP_858057.1
PITPNC1	XM_047435746.1	c.297+5898T>C		intron_variant	Intron 5 of 8		XP_047291702.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PITPNC1	ENST00000581322.6	c.366+5898T>C		intron_variant	Intron 5 of 8	1	NM_012417.4	ENSP00000464006.1
PITPNC1	ENST00000580974.6	c.366+5898T>C		intron_variant	Intron 5 of 9	1		ENSP00000463626.1
PITPNC1	ENST00000578527.1	n.504+5898T>C		intron_variant	Intron 2 of 6	1
PITPNC1	ENST00000581923.5	n.207+5898T>C		intron_variant	Intron 3 of 3	5

Frequencies

GnomAD3 genomes AF: 0.465 AC: 70546 AN: 151670 Hom.: 16690 Cov.: 30

Gnomad AFR AF: 0.510

Gnomad AMI AF: 0.452

Gnomad AMR AF: 0.493

Gnomad ASJ AF: 0.536

Gnomad EAS AF: 0.525

Gnomad SAS AF: 0.631

Gnomad FIN AF: 0.441

Gnomad MID AF: 0.522

Gnomad NFE AF: 0.415

Gnomad OTH AF: 0.463

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

GnomAD4 genome AF: 0.465 AC: 70594 AN: 151788 Hom.: 16696 Cov.: 30 AF XY: 0.471 AC XY: 34988 AN XY: 74212

Gnomad4 AFR AF: 0.510

Gnomad4 AMR AF: 0.493

Gnomad4 ASJ AF: 0.536

Gnomad4 EAS AF: 0.525

Gnomad4 SAS AF: 0.631

Gnomad4 FIN AF: 0.441

Gnomad4 NFE AF: 0.415

Gnomad4 OTH AF: 0.459

Alfa AF: 0.434 Hom.: 22831

Bravo AF: 0.473

Asia WGS AF: 0.584 AC: 2033 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	7.1
DANN	Benign	0.43

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: rs2570054; hg19: chr17-65580271;