Genetic Variant PID1:c.178-27197T>C (chr2-229053305-A-G) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is . The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001100818.2(PID1):c.178-27197T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.14 in 152,188 control chromosomes in the GnomAD database, including 2,167 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 ( 2167 hom., cov: 33)

Consequence

PID1
NM_001100818.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.23

Publications

0 publications found

Variant links:

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]

PID1 links:

Genome browser will be placed here

new If you want to explore the variant's impact on the transcript NM_001100818.2, check out the Mutation Effect Viewer. This is especially useful for frameshift variants or if you want to visualize the effect of exon loss / intron retention.

ACMG classification

Classification was made for transcript

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

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.62).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.261 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

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
PID1	NM_001100818.2	MANE Select	c.178-27197T>C	intron	N/A	NP_001094288.1	Q7Z2X4-4
PID1	NM_001330156.1		c.277-27197T>C	intron	N/A	NP_001317085.1	Q7Z2X4-1
PID1	NM_017933.5		c.271-27197T>C	intron	N/A	NP_060403.3

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
PID1	ENST00000392055.8	TSL:2 MANE Select	c.178-27197T>C	intron	N/A	ENSP00000375908.3	Q7Z2X4-4
PID1	ENST00000409462.1	TSL:1	c.31-27197T>C	intron	N/A	ENSP00000386826.1	Q7Z2X4-3
PID1	ENST00000354069.6	TSL:3	c.277-27197T>C	intron	N/A	ENSP00000283937.8	Q7Z2X4-1

Frequencies

GnomAD3 genomes

AF:

0.140

AC:

21287

AN:

152070

Hom.:

2157

Cov.:

show subpopulations

Gnomad AFR

AF:

0.266

Gnomad AMI

AF:

0.0691

Gnomad AMR

AF:

0.193

Gnomad ASJ

AF:

0.0616

Gnomad EAS

AF:

0.140

Gnomad SAS

AF:

0.122

Gnomad FIN

AF:

0.114

Gnomad MID

AF:

0.104

Gnomad NFE

AF:

0.0622

Gnomad OTH

AF:

0.134

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

GnomAD4 genome

AF:

0.140

AC:

21329

AN:

152188

Hom.:

2167

Cov.:

AF XY:

0.144

AC XY:

10709

AN XY:

74404

show subpopulations

African (AFR)

AF:

0.265

AC:

11017

AN:

41498

American (AMR)

AF:

0.194

AC:

2962

AN:

15274

Ashkenazi Jewish (ASJ)

AF:

0.0616

AC:

214

AN:

3472

East Asian (EAS)

AF:

0.139

AC:

719

AN:

5172

South Asian (SAS)

AF:

0.121

AC:

585

AN:

4826

European-Finnish (FIN)

AF:

0.114

AC:

1207

AN:

10606

Middle Eastern (MID)

AF:

0.105

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0622

AC:

4234

AN:

68022

Other (OTH)

AF:

0.141

AC:

297

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

863

1727

2590

3454

4317

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

220

440

660

880

1100

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.100

Hom.:

1621

Bravo

AF:

0.152

Asia WGS

AF:

0.173

AC:

600

AN:

3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.62

CADD

Benign

(source)

DANN

Benign

0.83

PhyloP100

1.2

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Publications

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over