NM_001100818.2:c.177+58110A>G

Variant names:

• chr2-229097708-T-C
• rs7589888
• NM_001100818.2:c.177+58110A>G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 1 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=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.759 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001100818.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PID1	NM_001100818.2	MANE Select	c.177+58110A>G		intron	N/A	NP_001094288.1
	PID1	NM_001330156.1		c.276+58110A>G		intron	N/A	NP_001317085.1
	PID1	NM_017933.5		c.270+58110A>G		intron	N/A	NP_060403.3

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PID1	ENST00000392055.8	TSL:2 MANE Select	c.177+58110A>G		intron	N/A	ENSP00000375908.3
	PID1	ENST00000409462.1	TSL:1	c.31-71600A>G		intron	N/A	ENSP00000386826.1
	PID1	ENST00000354069.6	TSL:3	c.276+58110A>G		intron	N/A	ENSP00000283937.8

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

African (AFR) AF: 0.300 AC: 12440 AN: 41454

American (AMR) AF: 0.611 AC: 9309 AN: 15226

Ashkenazi Jewish (ASJ) AF: 0.794 AC: 2755 AN: 3468

East Asian (EAS) AF: 0.676 AC: 3479 AN: 5146

South Asian (SAS) AF: 0.755 AC: 3634 AN: 4814

European-Finnish (FIN) AF: 0.687 AC: 7249 AN: 10546

Middle Eastern (MID) AF: 0.743 AC: 217 AN: 292

European-Non Finnish (NFE) AF: 0.764 AC: 51956 AN: 67972

Other (OTH) AF: 0.647 AC: 1366 AN: 2110

Alfa AF: 0.727 Hom.: 20110

Bravo AF: 0.595

Asia WGS AF: 0.646 AC: 2248 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.6
DANN	Benign	0.75
PhyloP100		-0.75
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs7589888; hg19: chr2-229962424;