Variant rs79201073 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_003119.4(SPG7):c.1449+19G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0696 in 1,613,508 control chromosomes in the GnomAD database, including 6,018 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.080 ( 663 hom., cov: 32)

Exomes 𝑓: 0.069 ( 5355 hom. )

Consequence

SPG7
NM_003119.4 intron

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:4

Conservation

PhyloP100: -0.718

Variant links:

Genes affected

SPG7 (HGNC:11237): (SPG7 matrix AAA peptidase subunit, paraplegin) This gene encodes a mitochondrial metalloprotease protein that is a member of the AAA family. Members of this protein family share an ATPase domain and have roles in diverse cellular processes including membrane trafficking, intracellular motility, organelle biogenesis, protein folding, and proteolysis. Mutations in this gene cause autosomal recessive spastic paraplegia 7. Two transcript variants encoding distinct isoforms have been identified. [provided by RefSeq, Mar 2014]

SPG7 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.83).

BP6

Variant 16-89544791-G-A is Benign according to our data. Variant chr16-89544791-G-A is described in ClinVar as [Benign]. Clinvar id is 258907.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr16-89544791-G-A is described in Lovd as [Benign].

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.299 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SPG7	NM_003119.4 linkuse as main transcript	c.1449+19G>A		intron_variant		ENST00000645818.2	NP_003110.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SPG7	ENST00000645818.2 linkuse as main transcript	c.1449+19G>A		intron_variant			NM_003119.4	ENSP00000495795	P2	Q9UQ90-1

Frequencies

GnomAD3 genomes

AF:

0.0797

AC:

12127

AN:

152166

Hom.:

663

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0694

Gnomad AMI

AF:

0.100

Gnomad AMR

AF:

0.0937

Gnomad ASJ

AF:

0.104

Gnomad EAS

AF:

0.312

Gnomad SAS

AF:

0.155

Gnomad FIN

AF:

0.0842

Gnomad MID

AF:

0.120

Gnomad NFE

AF:

0.0576

Gnomad OTH

AF:

0.0770

GnomAD3 exomes

AF:

0.102

AC:

25603

AN:

250906

Hom.:

1971

AF XY:

0.103

AC XY:

13987

AN XY:

135658

show subpopulations

Gnomad AFR exome

AF:

0.0662

Gnomad AMR exome

AF:

0.106

Gnomad ASJ exome

AF:

0.108

Gnomad EAS exome

AF:

0.325

Gnomad SAS exome

AF:

0.154

Gnomad FIN exome

AF:

0.0868

Gnomad NFE exome

AF:

0.0584

Gnomad OTH exome

AF:

0.0951

GnomAD4 exome

AF:

0.0686

AC:

100226

AN:

1461224

Hom.:

5355

Cov.:

AF XY:

0.0709

AC XY:

51538

AN XY:

726888

show subpopulations

Gnomad4 AFR exome

AF:

0.0694

Gnomad4 AMR exome

AF:

0.107

Gnomad4 ASJ exome

AF:

0.104

Gnomad4 EAS exome

AF:

0.306

Gnomad4 SAS exome

AF:

0.150

Gnomad4 FIN exome

AF:

0.0854

Gnomad4 NFE exome

AF:

0.0496

Gnomad4 OTH exome

AF:

0.0838

GnomAD4 genome

AF:

0.0797

AC:

12143

AN:

152284

Hom.:

663

Cov.:

AF XY:

0.0851

AC XY:

6336

AN XY:

74464

show subpopulations

Gnomad4 AFR

AF:

0.0696

Gnomad4 AMR

AF:

0.0937

Gnomad4 ASJ

AF:

0.104

Gnomad4 EAS

AF:

0.312

Gnomad4 SAS

AF:

0.155

Gnomad4 FIN

AF:

0.0842

Gnomad4 NFE

AF:

0.0576

Gnomad4 OTH

AF:

0.0762

Alfa

AF:

0.0708

Hom.:

123

Bravo

AF:

0.0798

Asia WGS

AF:

0.213

AC:

740

AN:

3476

ClinVar

Significance: Benign

Submissions summary: Benign:4

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	clinical testing	GeneDx	Mar 03, 2015	- -
Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -

not specified

Benign:1

Benign, criteria provided, single submitter

clinical testing

PreventionGenetics, part of Exact Sciences

- -

Hereditary spastic paraplegia 7

Benign:1

Benign, criteria provided, single submitter

clinical testing

Labcorp Genetics (formerly Invitae), Labcorp

Jan 31, 2024

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.83

CADD

Benign

0.61

DANN

Benign

0.63

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.0

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