17-1532956-G-A

Variant names:

• chr17-1532956-G-A
• rs17821234
• NM_006224.4:c.768+1143C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_006224.4(PITPNA):​c.768+1143C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0887 in 152,286 control chromosomes in the GnomAD database, including 808 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 0.089 (808 hom., cov: 32)
• Consequence: PITPNA NM_006224.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0890
• Publications: 3 publications found

Genes affected

PITPNA (HGNC:9001): (phosphatidylinositol transfer protein alpha) This gene encodes a member of a family of lipid-binding proteins that transfer molecules of phosphatidylinositol or phosphatidylcholine between membrane surfaces. The protein is implicated in phospholipase C signaling and in the production of phosphatidylinositol 3,4,5-trisphosphate (PIP3) by phosphoinositide-3-kinase.[provided by RefSeq, Sep 2009]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.132 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_006224.4. 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
	PITPNA	NM_006224.4	MANE Select	c.768+1143C>T		intron	N/A	NP_006215.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PITPNA	ENST00000313486.12	TSL:5 MANE Select	c.768+1143C>T		intron	N/A	ENSP00000316809.7
	PITPNA	ENST00000575288.5	TSL:2	n.*388+1143C>T		intron	N/A	ENSP00000461011.1

Frequencies

GnomAD3 genomes AF: 0.0889 AC: 13522 AN: 152168 Hom.: 811 Cov.: 32

Gnomad AFR AF: 0.0212

Gnomad AMI AF: 0.0978

Gnomad AMR AF: 0.0834

Gnomad ASJ AF: 0.135

Gnomad EAS AF: 0.141

Gnomad SAS AF: 0.0333

Gnomad FIN AF: 0.0934

Gnomad MID AF: 0.136

Gnomad NFE AF: 0.127

Gnomad OTH AF: 0.109

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

GnomAD4 genome AF: 0.0887 AC: 13514 AN: 152286 Hom.: 808 Cov.: 32 AF XY: 0.0854 AC XY: 6360 AN XY: 74464

African (AFR) AF: 0.0211 AC: 879 AN: 41584

American (AMR) AF: 0.0833 AC: 1274 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.135 AC: 468 AN: 3472

East Asian (EAS) AF: 0.141 AC: 728 AN: 5178

South Asian (SAS) AF: 0.0331 AC: 160 AN: 4828

European-Finnish (FIN) AF: 0.0934 AC: 990 AN: 10600

Middle Eastern (MID) AF: 0.133 AC: 39 AN: 294

European-Non Finnish (NFE) AF: 0.127 AC: 8660 AN: 68008

Other (OTH) AF: 0.107 AC: 227 AN: 2112

Alfa AF: 0.105 Hom.: 118

Bravo AF: 0.0869

Asia WGS AF: 0.0850 AC: 296 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	5.4
DANN	Benign	0.77
PhyloP100		0.089
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: rs17821234; hg19: chr17-1436250; COSMIC: COSV57933046; COSMIC: COSV57933046;