chr2-228859245-A-G

Variant names:

• chr2-228859245-A-G
• rs4487082
• ENST00000482518.6:n.357-8597T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000482518.6(PID1):​n.357-8597T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0478 in 152,242 control chromosomes in the GnomAD database, including 225 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 0.048 (225 hom., cov: 32)
• Consequence: PID1 ENST00000482518.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.727
• Publications: 4 publications found

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

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0746 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000482518.6. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PID1	ENST00000482518.6	TSL:2	n.357-8597T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0479 AC: 7284 AN: 152124 Hom.: 226 Cov.: 32

Gnomad AFR AF: 0.0143

Gnomad AMI AF: 0.0989

Gnomad AMR AF: 0.0415

Gnomad ASJ AF: 0.0383

Gnomad EAS AF: 0.00116

Gnomad SAS AF: 0.0396

Gnomad FIN AF: 0.0331

Gnomad MID AF: 0.00316

Gnomad NFE AF: 0.0763

Gnomad OTH AF: 0.0463

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

GnomAD4 genome AF: 0.0478 AC: 7279 AN: 152242 Hom.: 225 Cov.: 32 AF XY: 0.0445 AC XY: 3315 AN XY: 74432

African (AFR) AF: 0.0142 AC: 591 AN: 41556

American (AMR) AF: 0.0414 AC: 633 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.0383 AC: 133 AN: 3470

East Asian (EAS) AF: 0.00116 AC: 6 AN: 5172

South Asian (SAS) AF: 0.0390 AC: 188 AN: 4820

European-Finnish (FIN) AF: 0.0331 AC: 351 AN: 10608

Middle Eastern (MID) AF: 0.00340 AC: 1 AN: 294

European-Non Finnish (NFE) AF: 0.0763 AC: 5189 AN: 68012

Other (OTH) AF: 0.0458 AC: 97 AN: 2116

Alfa AF: 0.0640 Hom.: 273

Bravo AF: 0.0468

Asia WGS AF: 0.0180 AC: 64 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.25
DANN	Benign	0.56
PhyloP100		-0.73

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs4487082; hg19: chr2-229723961;