chr12-123017497-C-T

Position:

• chr12-123017497-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_020845.3(PITPNM2):​c.79-3455G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.543 in 152,114 control chromosomes in the GnomAD database, including 26,979 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 0.54 (26979 hom., cov: 33)
• Consequence: PITPNM2 NM_020845.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.174

Genes affected

PITPNM2 (HGNC:21044): (phosphatidylinositol transfer protein membrane associated 2) PITPNM2 belongs to a family of membrane-associated phosphatidylinositol transfer domain-containing proteins that share homology with the Drosophila retinal degeneration B (rdgB) protein (Ocaka et al., 2005 [PubMed 15627748]).[supplied by OMIM, Mar 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.702 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PITPNM2	NM_020845.3	c.79-3455G>A		intron_variant		ENST00000320201.10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PITPNM2	ENST00000320201.10	c.79-3455G>A		intron_variant		5	NM_020845.3	P3

Frequencies

GnomAD3 genomes AF: 0.544 AC: 82674 AN: 151996 Hom.: 26986 Cov.: 33

Gnomad AFR AF: 0.161

Gnomad AMI AF: 0.747

Gnomad AMR AF: 0.640

Gnomad ASJ AF: 0.619

Gnomad EAS AF: 0.675

Gnomad SAS AF: 0.577

Gnomad FIN AF: 0.719

Gnomad MID AF: 0.570

Gnomad NFE AF: 0.708

Gnomad OTH AF: 0.582

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

GnomAD4 genome AF: 0.543 AC: 82664 AN: 152114 Hom.: 26979 Cov.: 33 AF XY: 0.547 AC XY: 40694 AN XY: 74362

Gnomad4 AFR AF: 0.161

Gnomad4 AMR AF: 0.639

Gnomad4 ASJ AF: 0.619

Gnomad4 EAS AF: 0.675

Gnomad4 SAS AF: 0.578

Gnomad4 FIN AF: 0.719

Gnomad4 NFE AF: 0.708

Gnomad4 OTH AF: 0.580

Alfa AF: 0.493 Hom.: 2412

Bravo AF: 0.517

Asia WGS AF: 0.564 AC: 1961 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	14
DANN	Benign	0.38
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1

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: rs12425009; hg19: chr12-123502044;