NM_012417.4:c.48+36616A>G

Variant names:

• chr17-67414818-A-G
• rs7224000
• NM_012417.4:c.48+36616A>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.48+36616A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.489 in 151,982 control chromosomes in the GnomAD database, including 18,701 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 0.49 (18701 hom., cov: 32)
• Consequence: PITPNC1 NM_012417.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.177
• Publications: 6 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]

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 = 0.6 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PITPNC1	NM_012417.4	c.48+36616A>G		intron_variant	Intron 1 of 8	ENST00000581322.6	NP_036549.2
PITPNC1	NM_181671.3	c.48+36616A>G		intron_variant	Intron 1 of 9		NP_858057.1
PITPNC1	XM_047435746.1	c.-22+23797A>G		intron_variant	Intron 1 of 8		XP_047291702.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PITPNC1	ENST00000581322.6	c.48+36616A>G		intron_variant	Intron 1 of 8	1	NM_012417.4	ENSP00000464006.1
PITPNC1	ENST00000580974.6	c.48+36616A>G		intron_variant	Intron 1 of 9	1		ENSP00000463626.1
PITPNC1	ENST00000584471.5	c.-22+35426A>G		intron_variant	Intron 1 of 4	5		ENSP00000464584.1

Frequencies

GnomAD3 genomes AF: 0.488 AC: 74147 AN: 151864 Hom.: 18659 Cov.: 32

Gnomad AFR AF: 0.607

Gnomad AMI AF: 0.488

Gnomad AMR AF: 0.490

Gnomad ASJ AF: 0.535

Gnomad EAS AF: 0.264

Gnomad SAS AF: 0.448

Gnomad FIN AF: 0.396

Gnomad MID AF: 0.538

Gnomad NFE AF: 0.447

Gnomad OTH AF: 0.510

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

GnomAD4 genome AF: 0.489 AC: 74250 AN: 151982 Hom.: 18701 Cov.: 32 AF XY: 0.487 AC XY: 36202 AN XY: 74322

African (AFR) AF: 0.607 AC: 25148 AN: 41446

American (AMR) AF: 0.491 AC: 7489 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.535 AC: 1857 AN: 3470

East Asian (EAS) AF: 0.265 AC: 1370 AN: 5176

South Asian (SAS) AF: 0.447 AC: 2152 AN: 4810

European-Finnish (FIN) AF: 0.396 AC: 4177 AN: 10560

Middle Eastern (MID) AF: 0.558 AC: 164 AN: 294

European-Non Finnish (NFE) AF: 0.447 AC: 30366 AN: 67940

Other (OTH) AF: 0.513 AC: 1083 AN: 2112

Alfa AF: 0.463 Hom.: 64728

Bravo AF: 0.501

Asia WGS AF: 0.441 AC: 1530 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	1.6
DANN	Benign	0.48
PhyloP100		0.18
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: rs7224000; hg19: chr17-65410934;