Variant chr2-229271028-T-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_StrongBP6BS2

The NM_001100818.2(PID1):c.16A>G(p.Thr6Ala) variant causes a missense change. The variant allele was found at a frequency of 0.000322 in 1,543,192 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (no stars).

Frequency

Genomes: 𝑓 0.00025 ( 0 hom., cov: 31)

Exomes 𝑓: 0.00033 ( 2 hom. )

Consequence

PID1
NM_001100818.2 missense

Scores

Clinical Significance

Likely benign no assertion criteria provided B:1

Conservation

PhyloP100: 3.85

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

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -9 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.007999629).

BP6

Variant 2-229271028-T-C is Benign according to our data. Variant chr2-229271028-T-C is described in ClinVar as [Likely_benign]. Clinvar id is 3033804.Status of the report is no_assertion_criteria_provided, 0 stars.

BS2

High Homozygotes in GnomAdExome4 at 2 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE
PID1	NM_001100818.2 linkuse as main transcript	c.16A>G	p.Thr6Ala	missense_variant	1/3	ENST00000392055.8
PID1	NM_001330157.2 linkuse as main transcript	c.16A>G	p.Thr6Ala	missense_variant	1/2
PID1	NM_001330158.2 linkuse as main transcript	c.-134A>G		5_prime_UTR_variant	1/4
PID1	NM_017933.5 linkuse as main transcript	c.-103A>G		5_prime_UTR_variant	1/4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PID1	ENST00000392055.8 linkuse as main transcript	c.16A>G	p.Thr6Ala	missense_variant	1/3	2	NM_001100818.2	P1	Q7Z2X4-4
PID1	ENST00000409462.1 linkuse as main transcript	c.16A>G	p.Thr6Ala	missense_variant	1/2	1			Q7Z2X4-3
PID1	ENST00000392054.7 linkuse as main transcript	c.-103A>G		5_prime_UTR_variant	1/4	2			Q7Z2X4-2
PID1	ENST00000534952.1 linkuse as main transcript	c.16A>G	p.Thr6Ala	missense_variant, NMD_transcript_variant	1/4	4

Frequencies

GnomAD3 genomes

AF:

0.000250

AC:

AN:

152032

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0000241

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0000655

Gnomad ASJ

AF:

0.00202

Gnomad EAS

AF:

0.000195

Gnomad SAS

AF:

0.00228

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.000221

Gnomad OTH

AF:

0.000958

GnomAD3 exomes

AF:

0.000661

AC:

AN:

143668

Hom.:

AF XY:

0.000790

AC XY:

AN XY:

77258

show subpopulations

Gnomad AFR exome

AF:

0.00

Gnomad AMR exome

AF:

0.0000848

Gnomad ASJ exome

AF:

0.00171

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.00260

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.000316

Gnomad OTH exome

AF:

0.000983

GnomAD4 exome

AF:

0.000330

AC:

459

AN:

1391042

Hom.:

Cov.:

AF XY:

0.000404

AC XY:

277

AN XY:

686178

show subpopulations

Gnomad4 AFR exome

AF:

0.00

Gnomad4 AMR exome

AF:

0.000142

Gnomad4 ASJ exome

AF:

0.00160

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.00282

Gnomad4 FIN exome

AF:

0.00

Gnomad4 NFE exome

AF:

0.000151

Gnomad4 OTH exome

AF:

0.000452

GnomAD4 genome

AF:

0.000250

AC:

AN:

152150

Hom.:

Cov.:

AF XY:

0.000255

AC XY:

AN XY:

74372

show subpopulations

Gnomad4 AFR

AF:

0.0000241

Gnomad4 AMR

AF:

0.0000654

Gnomad4 ASJ

AF:

0.00202

Gnomad4 EAS

AF:

0.000196

Gnomad4 SAS

AF:

0.00228

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.000221

Gnomad4 OTH

AF:

0.000948

Alfa

AF:

0.000276

Hom.:

Bravo

AF:

0.000174

ExAC

AF:

0.000518

AC:

Asia WGS

AF:

0.000577

AC:

AN:

3478

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: no assertion criteria provided

LINK: link

Submissions by phenotype

PID1-related disorder

Benign:1

Likely benign, no assertion criteria provided

clinical testing

PreventionGenetics, part of Exact Sciences

Nov 01, 2022

This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_addAF

Benign

-0.38

BayesDel_noAF

Benign

-0.32

CADD

Benign

DANN

Uncertain

0.98

Eigen

Uncertain

0.19

Eigen_PC

Uncertain

0.26

FATHMM_MKL

Uncertain

0.88

LIST_S2

Benign

0.32

T;T

M_CAP

Uncertain

0.16

MetaRNN

Benign

0.0080

T;T

MetaSVM

Benign

-0.90

MutationTaster

Benign

1.0

D;N;N

PROVEAN

Benign

-0.39

N;N

REVEL

Benign

0.066

Sift

Benign

0.35

T;T

Sift4G

Benign

0.70

T;T

Polyphen

0.59

P;P

Vest4

0.24

MVP

0.17

ClinPred

0.040

GERP RS

4.6

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over