chr2-229028032-G-A

Position:

• chr2-229028032-G-A

Variant summary

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

The NM_001100818.2(PID1):​c.178-1924C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.136 in 152,068 control chromosomes in the GnomAD database, including 1,448 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 0.14 (1448 hom., cov: 32)
• Consequence: PID1 NM_001100818.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.597

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=-0.93).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.171 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PID1	NM_001100818.2	c.178-1924C>T		intron_variant		ENST00000392055.8	NP_001094288.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PID1	ENST00000392055.8	c.178-1924C>T		intron_variant		2	NM_001100818.2	ENSP00000375908	P1

Frequencies

GnomAD3 genomes AF: 0.136 AC: 20738 AN: 151950 Hom.: 1446 Cov.: 32

Gnomad AFR AF: 0.129

Gnomad AMI AF: 0.186

Gnomad AMR AF: 0.177

Gnomad ASJ AF: 0.186

Gnomad EAS AF: 0.111

Gnomad SAS AF: 0.0796

Gnomad FIN AF: 0.123

Gnomad MID AF: 0.105

Gnomad NFE AF: 0.137

Gnomad OTH AF: 0.126

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

GnomAD4 genome AF: 0.136 AC: 20757 AN: 152068 Hom.: 1448 Cov.: 32 AF XY: 0.134 AC XY: 9937 AN XY: 74364

Gnomad4 AFR AF: 0.128

Gnomad4 AMR AF: 0.177

Gnomad4 ASJ AF: 0.186

Gnomad4 EAS AF: 0.111

Gnomad4 SAS AF: 0.0798

Gnomad4 FIN AF: 0.123

Gnomad4 NFE AF: 0.137

Gnomad4 OTH AF: 0.132

Alfa AF: 0.139 Hom.: 192

Bravo AF: 0.140

Asia WGS AF: 0.124 AC: 431 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.51
DANN	Benign	0.31

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: rs7580152; hg19: chr2-229892748;