17-6455662-G-T

Variant names:

• chr17-6455662-G-T
• rs373992381
• NM_031220.4:c.2620-19C>A

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Strong BP6_Moderate BS2

The NM_031220.4(PITPNM3):​c.2620-19C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000237 in 1,474,030 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.000025 (0 hom., cov: 0)
  • Exomes 𝑓: 0.000024 (0 hom.)
• Consequence: PITPNM3 NM_031220.4 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.164
• Publications: 0 publications found

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]

PITPNM3 Gene-Disease associations (from GenCC):

• cone-rod dystrophy 5

  Inheritance: AD Classification: STRONG, LIMITED Submitted by: G2P, Labcorp Genetics (formerly Invitae)
• cone-rod dystrophy

  Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BP6: Variant 17-6455662-G-T is Benign according to our data. Variant chr17-6455662-G-T is described in ClinVar as Benign. ClinVar VariationId is 261947.Status of the report is criteria_provided_single_submitter, 1 stars.
• BS2: High AC in GnomAdExome4 at 34 AD gene.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_031220.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PITPNM3	NM_031220.4	MANE Select	c.2620-19C>A		intron	N/A	NP_112497.2	Q9BZ71-1
	PITPNM3	NM_001165966.2		c.2512-19C>A		intron	N/A	NP_001159438.1	Q9BZ71-3

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PITPNM3	ENST00000262483.13	TSL:1 MANE Select	c.2620-19C>A		intron	N/A	ENSP00000262483.8	Q9BZ71-1
	PITPNM3	ENST00000572795.1	TSL:1	n.5126-19C>A		intron	N/A
	PITPNM3	ENST00000576664.5	TSL:1	n.1369-19C>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0000248 AC: 1 AN: 40292 Hom.: 0 Cov.: 0

Gnomad AFR AF: 0.00

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0000547

Gnomad OTH AF: 0.00

GnomAD2 exomes AF: 0.0000464 AC: 10 AN: 215720 AF XY: 0.0000416

Gnomad AFR exome AF: 0.00

Gnomad AMR exome AF: 0.00

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.00

Gnomad FIN exome AF: 0.0000951

Gnomad NFE exome AF: 0.0000910

Gnomad OTH exome AF: 0.00

GnomAD4 exome AF: 0.0000237 AC: 34 AN: 1433738 Hom.: 0 Cov.: 35 AF XY: 0.0000280 AC XY: 20 AN XY: 713718

African (AFR) AF: 0.00 AC: 0 AN: 33042

American (AMR) AF: 0.0000226 AC: 1 AN: 44198

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 25800

East Asian (EAS) AF: 0.00 AC: 0 AN: 39302

South Asian (SAS) AF: 0.00 AC: 0 AN: 85468

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 37346

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 5108

European-Non Finnish (NFE) AF: 0.0000272 AC: 30 AN: 1103880

Other (OTH) AF: 0.0000503 AC: 3 AN: 59594

GnomAD4 genome AF: 0.0000248 AC: 1 AN: 40292 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 19718

African (AFR) AF: 0.00 AC: 0 AN: 10730

American (AMR) AF: 0.00 AC: 0 AN: 3084

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 814

East Asian (EAS) AF: 0.00 AC: 0 AN: 2416

South Asian (SAS) AF: 0.00 AC: 0 AN: 1498

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 2698

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 84

European-Non Finnish (NFE) AF: 0.0000547 AC: 1 AN: 18280

Other (OTH) AF: 0.00 AC: 0 AN: 480

Alfa AF: 0.000119 Hom.: 0

ClinVar

ClinVar submissions

Significance: Benign

Revision: criteria provided, single submitter

Pathogenic	VUS	Benign	Condition
-	-	1	not specified (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	3.6
DANN	Benign	0.72
PhyloP100		0.16

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: rs373992381; hg19: chr17-6358982;