rs73346359

chr17-6461561-T-C

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_Strong BP6_Very_Strong BA1

The NM_031220.4(PITPNM3):c.2307-5A>G variant causes a splice region, splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0577 in 1,613,868 control chromosomes in the GnomAD database, including 3,574 homozygotes. In-silico tool predicts a benign outcome for this variant. 2/2 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Benign (★★).

• Frequency:
  • Genomes: 𝑓 0.083 (730 hom., cov: 33)
  • Exomes 𝑓: 0.055 (2844 hom.)
• Consequence: PITPNM3 NM_031220.4 splice_region, splice_polypyrimidine_tract, intron
• Scores: Splicing: ADA: 0.00003512
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:4
• Conservation: PhyloP100: -1.21

Genes affected

PITPNM3 (HGNC:21043): (PITPNM family member 3) This gene encodes a member of a family of membrane-associated phosphatidylinositol transfer domain-containing proteins. The calcium-binding protein has phosphatidylinositol (PI) transfer activity and interacts with the protein tyrosine kinase PTK2B (also known as PYK2). The protein is homologous to a Drosophila protein that is implicated in the visual transduction pathway in flies. Mutations in this gene result in autosomal dominant cone dystrophy. Multiple transcript variants encoding different isoforms have been found for this gene.[provided by RefSeq, Sep 2009]

ACMG classification

Verdict is Benign. Variant got -20 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BP6: Variant 17-6461561-T-C is Benign according to our data. Variant chr17-6461561-T-C is described in ClinVar as [Benign]. Clinvar id is 261944.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.16 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PITPNM3	NM_031220.4	c.2307-5A>G		splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant		ENST00000262483.13
PITPNM3	NM_001165966.2	c.2199-5A>G		splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant
PITPNM3	XM_011524015.4	c.2307-5A>G		splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PITPNM3	ENST00000262483.13	c.2307-5A>G		splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant		1	NM_031220.4	P1

Frequencies

GnomAD3 genomes AF: 0.0832 AC: 12653 AN: 152140 Hom.: 719 Cov.: 33

Gnomad AFR AF: 0.159

Gnomad AMI AF: 0.0440

Gnomad AMR AF: 0.0386

Gnomad ASJ AF: 0.0170

Gnomad EAS AF: 0.168

Gnomad SAS AF: 0.0488

Gnomad FIN AF: 0.0663

Gnomad MID AF: 0.0411

Gnomad NFE AF: 0.0505

Gnomad OTH AF: 0.0611

GnomAD3 exomes AF: 0.0594 AC: 14933 AN: 251260 Hom.: 702 AF XY: 0.0575 AC XY: 7803 AN XY: 135800

Gnomad AFR exome AF: 0.158

Gnomad AMR exome AF: 0.0228

Gnomad ASJ exome AF: 0.0146

Gnomad EAS exome AF: 0.162

Gnomad SAS exome AF: 0.0469

Gnomad FIN exome AF: 0.0657

Gnomad NFE exome AF: 0.0467

Gnomad OTH exome AF: 0.0458

GnomAD4 exome AF: 0.0551 AC: 80495 AN: 1461610 Hom.: 2844 Cov.: 36 AF XY: 0.0543 AC XY: 39487 AN XY: 727116

Gnomad4 AFR exome AF: 0.164

Gnomad4 AMR exome AF: 0.0239

Gnomad4 ASJ exome AF: 0.0165

Gnomad4 EAS exome AF: 0.156

Gnomad4 SAS exome AF: 0.0451

Gnomad4 FIN exome AF: 0.0643

Gnomad4 NFE exome AF: 0.0507

Gnomad4 OTH exome AF: 0.0575

GnomAD4 genome AF: 0.0834 AC: 12705 AN: 152258 Hom.: 730 Cov.: 33 AF XY: 0.0833 AC XY: 6202 AN XY: 74454

Gnomad4 AFR AF: 0.160

Gnomad4 AMR AF: 0.0385

Gnomad4 ASJ AF: 0.0170

Gnomad4 EAS AF: 0.169

Gnomad4 SAS AF: 0.0487

Gnomad4 FIN AF: 0.0663

Gnomad4 NFE AF: 0.0505

Gnomad4 OTH AF: 0.0624

Alfa AF: 0.0592 Hom.: 194

Bravo AF: 0.0840

Asia WGS AF: 0.124 AC: 430 AN: 3478

EpiCase AF: 0.0435

EpiControl AF: 0.0438

ClinVar

Significance: Benign

Submissions summary: Benign:4

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

not provided Benign:2

Benign, criteria provided, single submitter	clinical testing	Invitae	Jan 31, 2024	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Aug 30, 2018	- -

not specified Benign:1

Benign, criteria provided, single submitter

clinical testing

PreventionGenetics, part of Exact Sciences

-

- -

Cone-rod dystrophy 5 Benign:1

Benign, criteria provided, single submitter

clinical testing

Illumina Laboratory Services, Illumina

Jan 13, 2018

This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
Cadd	Benign	0.015
Dann	Benign	0.56

Splicing

Name	Calibrated prediction	Score	Prediction
dbscSNV1_ADA	Benign	0.000035
dbscSNV1_RF	Benign	0.012
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: rs73346359; hg19: chr17-6364881; COSMIC: COSV52593002;