chr2-228859245-A-G

Position:

• chr2-228859245-A-G

Variant summary

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

The ENST00000482518.6(PID1):​n.357-8597T>C variant causes a intron, non coding transcript 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, non_coding_transcript
• 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=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0746 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PID1	ENST00000482518.6	n.357-8597T>C		intron_variant, non_coding_transcript_variant		2

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

Gnomad4 AFR AF: 0.0142

Gnomad4 AMR AF: 0.0414

Gnomad4 ASJ AF: 0.0383

Gnomad4 EAS AF: 0.00116

Gnomad4 SAS AF: 0.0390

Gnomad4 FIN AF: 0.0331

Gnomad4 NFE AF: 0.0763

Gnomad4 OTH AF: 0.0458

Alfa AF: 0.0671 Hom.: 181

Bravo AF: 0.0468

Asia WGS AF: 0.0180 AC: 64 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4487082; hg19: chr2-229723961;