Variant chr11-47571628-G-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 2P and 16B. PM4BP6_Very_StrongBS1BS2

The NM_175732.3(PTPMT1):c.605G>C(p.Ter202SerextTer38) variant causes a stop lost change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00439 in 1,613,928 control chromosomes in the GnomAD database, including 45 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.0033 ( 5 hom., cov: 32)

Exomes 𝑓: 0.0045 ( 40 hom. )

Consequence

PTPMT1
NM_175732.3 stop_lost

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: 1.48

Variant links:

Genes affected

PTPMT1 (HGNC:26965): (protein tyrosine phosphatase mitochondrial 1) Predicted to enable phosphatidylglycerophosphatase activity and phosphatidylinositol-4,5-bisphosphate 5-phosphatase activity. Involved in regulation of intrinsic apoptotic signaling pathway. Located in mitochondrion. [provided by Alliance of Genome Resources, Apr 2022]

PTPMT1 links:

NDUFS3 (HGNC:7710): (NADH:ubiquinone oxidoreductase core subunit S3) This gene encodes one of the iron-sulfur protein (IP) components of mitochondrial NADH:ubiquinone oxidoreductase (complex I). Mutations in this gene are associated with Leigh syndrome resulting from mitochondrial complex I deficiency.[provided by RefSeq, Apr 2009]

NDUFS3 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

PM4

Stoplost variant in NM_175732.3 Downstream stopcodon found after 209 codons.

BP6

Variant 11-47571628-G-C is Benign according to our data. Variant chr11-47571628-G-C is described in ClinVar as [Benign]. Clinvar id is 720436.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BS1

Variant frequency is greater than expected in population sas. gnomad4_exome allele frequency = 0.0045 (6578/1461672) while in subpopulation SAS AF= 0.0216 (1867/86244). AF 95% confidence interval is 0.0208. There are 40 homozygotes in gnomad4_exome. There are 3634 alleles in male gnomad4_exome subpopulation. Median coverage is 30. This position pass quality control queck.

BS2

High AC in GnomAd4 at 502 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PTPMT1	NM_175732.3 linkuse as main transcript	c.605G>C	p.Ter202SerextTer38	stop_lost	4/4	ENST00000326674.10
PTPMT1	NM_001143984.2 linkuse as main transcript	c.*66G>C		3_prime_UTR_variant	2/2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PTPMT1	ENST00000326674.10 linkuse as main transcript	c.605G>C	p.Ter202SerextTer38	stop_lost	4/4	1	NM_175732.3	P1	Q8WUK0-1

Frequencies

GnomAD3 genomes

AF:

0.00331

AC:

504

AN:

152138

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000627

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00642

Gnomad ASJ

AF:

0.00749

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.0178

Gnomad FIN

AF:

0.0000943

Gnomad MID

AF:

0.00316

Gnomad NFE

AF:

0.00381

Gnomad OTH

AF:

0.00335

GnomAD3 exomes

AF:

0.00507

AC:

1263

AN:

249274

Hom.:

AF XY:

0.00602

AC XY:

814

AN XY:

135238

show subpopulations

Gnomad AFR exome

AF:

0.000387

Gnomad AMR exome

AF:

0.00279

Gnomad ASJ exome

AF:

0.00616

Gnomad EAS exome

AF:

0.000111

Gnomad SAS exome

AF:

0.0215

Gnomad FIN exome

AF:

0.000418

Gnomad NFE exome

AF:

0.00360

Gnomad OTH exome

AF:

0.00396

GnomAD4 exome

AF:

0.00450

AC:

6578

AN:

1461672

Hom.:

Cov.:

AF XY:

0.00500

AC XY:

3634

AN XY:

727138

show subpopulations

Gnomad4 AFR exome

AF:

0.000299

Gnomad4 AMR exome

AF:

0.00338

Gnomad4 ASJ exome

AF:

0.00586

Gnomad4 EAS exome

AF:

0.0000252

Gnomad4 SAS exome

AF:

0.0216

Gnomad4 FIN exome

AF:

0.000337

Gnomad4 NFE exome

AF:

0.00358

Gnomad4 OTH exome

AF:

0.00573

GnomAD4 genome

AF:

0.00330

AC:

502

AN:

152256

Hom.:

Cov.:

AF XY:

0.00360

AC XY:

268

AN XY:

74430

show subpopulations

Gnomad4 AFR

AF:

0.000625

Gnomad4 AMR

AF:

0.00642

Gnomad4 ASJ

AF:

0.00749

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.0176

Gnomad4 FIN

AF:

0.0000943

Gnomad4 NFE

AF:

0.00381

Gnomad4 OTH

AF:

0.00284

Alfa

AF:

0.00359

Hom.:

Bravo

AF:

0.00347

TwinsUK

AF:

0.00405

AC:

ALSPAC

AF:

0.00389

AC:

ESP6500AA

AF:

0.00107

AC:

ESP6500EA

AF:

0.00425

AC:

ExAC

AF:

0.00481

AC:

581

Asia WGS

AF:

0.00779

AC:

AN:

3478

EpiCase

AF:

0.00344

EpiControl

AF:

0.00462

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Aug 22, 2018	- -
Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_addAF

Benign

-0.71

BayesDel_noAF

Benign

-0.77

CADD

Benign

DANN

Benign

0.81

Eigen

Uncertain

0.43

Eigen_PC

Benign

0.12

FATHMM_MKL

Benign

0.24

MutationTaster

Benign

1.0

N;N;N;N

Vest4

0.019

GERP RS

3.8

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.7

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