2-229097708-T-C

Position:

• chr2-229097708-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+58110A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.613 in 151,940 control chromosomes in the GnomAD database, including 31,525 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 0.61 (31525 hom., cov: 32)
• Consequence: PID1 NM_001100818.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.753

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=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.759 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PID1	NM_001100818.2	c.177+58110A>G		intron_variant		ENST00000392055.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PID1	ENST00000392055.8	c.177+58110A>G		intron_variant		2	NM_001100818.2	P1

Frequencies

GnomAD3 genomes AF: 0.613 AC: 93058 AN: 151820 Hom.: 31517 Cov.: 32

Gnomad AFR AF: 0.300

Gnomad AMI AF: 0.759

Gnomad AMR AF: 0.611

Gnomad ASJ AF: 0.794

Gnomad EAS AF: 0.676

Gnomad SAS AF: 0.755

Gnomad FIN AF: 0.687

Gnomad MID AF: 0.756

Gnomad NFE AF: 0.764

Gnomad OTH AF: 0.646

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

GnomAD4 genome AF: 0.613 AC: 93097 AN: 151940 Hom.: 31525 Cov.: 32 AF XY: 0.613 AC XY: 45475 AN XY: 74244

Gnomad4 AFR AF: 0.300

Gnomad4 AMR AF: 0.611

Gnomad4 ASJ AF: 0.794

Gnomad4 EAS AF: 0.676

Gnomad4 SAS AF: 0.755

Gnomad4 FIN AF: 0.687

Gnomad4 NFE AF: 0.764

Gnomad4 OTH AF: 0.647

Alfa AF: 0.725 Hom.: 17943

Bravo AF: 0.595

Asia WGS AF: 0.646 AC: 2248 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.6
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: rs7589888; hg19: chr2-229962424;