chr2-229105082-A-G

Position:

• chr2-229105082-A-G

Variant summary

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

The NM_001100818.2(PID1):​c.177+50736T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.298 in 152,170 control chromosomes in the GnomAD database, including 6,939 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 0.30 (6939 hom., cov: 33)
• Consequence: PID1 NM_001100818.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.336

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=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.35 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PID1	NM_001100818.2	c.177+50736T>C		intron_variant		ENST00000392055.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PID1	ENST00000392055.8	c.177+50736T>C		intron_variant		2	NM_001100818.2	P1

Frequencies

GnomAD3 genomes AF: 0.298 AC: 45370 AN: 152052 Hom.: 6944 Cov.: 33

Gnomad AFR AF: 0.356

Gnomad AMI AF: 0.0987

Gnomad AMR AF: 0.328

Gnomad ASJ AF: 0.218

Gnomad EAS AF: 0.364

Gnomad SAS AF: 0.343

Gnomad FIN AF: 0.278

Gnomad MID AF: 0.296

Gnomad NFE AF: 0.259

Gnomad OTH AF: 0.295

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

GnomAD4 genome AF: 0.298 AC: 45386 AN: 152170 Hom.: 6939 Cov.: 33 AF XY: 0.301 AC XY: 22409 AN XY: 74398

Gnomad4 AFR AF: 0.355

Gnomad4 AMR AF: 0.328

Gnomad4 ASJ AF: 0.218

Gnomad4 EAS AF: 0.364

Gnomad4 SAS AF: 0.342

Gnomad4 FIN AF: 0.278

Gnomad4 NFE AF: 0.259

Gnomad4 OTH AF: 0.293

Alfa AF: 0.266 Hom.: 8709

Bravo AF: 0.302

Asia WGS AF: 0.326 AC: 1130 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	5.0
DANN	Benign	0.61

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: rs6436839; hg19: chr2-229969798;