17-6451782-GT-G

Position:

• chr17-6451782-GT-G

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_Moderate BA1

The NM_031220.4(PITPNM3):​c.*3555del variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.90 (60964 hom., cov: 0)
  • Exomes 𝑓: 0.83 (8 hom.)
• Consequence: PITPNM3 NM_031220.4 3_prime_UTR
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.604

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 -10 ACMG points.

• BP6: Variant 17-6451782-GT-G is Benign according to our data. Variant chr17-6451782-GT-G is described in ClinVar as [Benign]. Clinvar id is 324659.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.941 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PITPNM3	NM_031220.4	c.*3555del		3_prime_UTR_variant	20/20	ENST00000262483.13	NP_112497.2
PITPNM3	NM_001165966.2	c.*3555del		3_prime_UTR_variant	19/19		NP_001159438.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PITPNM3	ENST00000262483.13	c.*3555del		3_prime_UTR_variant	20/20	1	NM_031220.4	ENSP00000262483	P1
PITPNM3	ENST00000421306.7	c.*3555del		3_prime_UTR_variant	19/19	2		ENSP00000407882

Frequencies

GnomAD3 genomes AF: 0.895 AC: 135661 AN: 151506 Hom.: 60917 Cov.: 0

Gnomad AFR AF: 0.948

Gnomad AMI AF: 0.897

Gnomad AMR AF: 0.877

Gnomad ASJ AF: 0.876

Gnomad EAS AF: 0.853

Gnomad SAS AF: 0.857

Gnomad FIN AF: 0.859

Gnomad MID AF: 0.908

Gnomad NFE AF: 0.880

Gnomad OTH AF: 0.890

GnomAD4 exome AF: 0.833 AC: 20 AN: 24 Hom.: 8 Cov.: 0 AF XY: 0.850 AC XY: 17 AN XY: 20

Gnomad4 EAS exome AF: 1.00

Gnomad4 NFE exome AF: 0.850

GnomAD4 genome AF: 0.895 AC: 135765 AN: 151622 Hom.: 60964 Cov.: 0 AF XY: 0.895 AC XY: 66264 AN XY: 74044

Gnomad4 AFR AF: 0.948

Gnomad4 AMR AF: 0.877

Gnomad4 ASJ AF: 0.876

Gnomad4 EAS AF: 0.853

Gnomad4 SAS AF: 0.856

Gnomad4 FIN AF: 0.859

Gnomad4 NFE AF: 0.880

Gnomad4 OTH AF: 0.890

Alfa AF: 0.890 Hom.: 6462

Bravo AF: 0.893

Asia WGS AF: 0.848 AC: 2949 AN: 3476

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

Cone-Rod Dystrophy, Dominant Benign:1

Benign, criteria provided, single submitter

clinical testing

Illumina Laboratory Services, Illumina

Jun 14, 2016

- -

Computational scores

Source: dbNSFP v4.3

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: rs61555153; hg19: chr17-6355102;