rs12467995

chr2-229129653-T-C

Variant summary

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

The NM_001100818.2(PID1):c.177+26165A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0693 in 152,264 control chromosomes in the GnomAD database, including 543 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 0.069 (543 hom., cov: 32)
• Consequence: PID1 NM_001100818.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.727

Genes affected

PID1 (HGNC:26084): (phosphotyrosine interaction domain containing 1) Involved in several processes, including mitochondrion morphogenesis; negative regulation of phosphate metabolic process; and positive regulation of macromolecule metabolic process. Located in cytoplasm. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.211 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PID1	NM_001100818.2	c.177+26165A>G		intron_variant		ENST00000392055.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PID1	ENST00000392055.8	c.177+26165A>G		intron_variant		2	NM_001100818.2	P1

Frequencies

GnomAD3 genomes AF: 0.0693 AC: 10537 AN: 152146 Hom.: 538 Cov.: 32

Gnomad AFR AF: 0.0162

Gnomad AMI AF: 0.0297

Gnomad AMR AF: 0.0599

Gnomad ASJ AF: 0.0757

Gnomad EAS AF: 0.207

Gnomad SAS AF: 0.223

Gnomad FIN AF: 0.0811

Gnomad MID AF: 0.0316

Gnomad NFE AF: 0.0807

Gnomad OTH AF: 0.0750

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

GnomAD4 genome AF: 0.0693 AC: 10545 AN: 152264 Hom.: 543 Cov.: 32 AF XY: 0.0729 AC XY: 5427 AN XY: 74428

Gnomad4 AFR AF: 0.0162

Gnomad4 AMR AF: 0.0607

Gnomad4 ASJ AF: 0.0757

Gnomad4 EAS AF: 0.207

Gnomad4 SAS AF: 0.222

Gnomad4 FIN AF: 0.0811

Gnomad4 NFE AF: 0.0807

Gnomad4 OTH AF: 0.0752

Alfa AF: 0.0858 Hom.: 322

Bravo AF: 0.0625

Asia WGS AF: 0.208 AC: 720 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
Cadd	Benign	0.16
Dann	Benign	0.75

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: rs12467995; hg19: chr2-229994369;