Variant 14-88391362-T-G 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_018418.5(SPATA7):c.20-19T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0849 in 1,601,378 control chromosomes in the GnomAD database, including 6,698 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.067 ( 499 hom., cov: 32)

Exomes 𝑓: 0.087 ( 6199 hom. )

Consequence

SPATA7
NM_018418.5 intron

Scores

Clinical Significance

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

Conservation

PhyloP100: -0.00600

Variant links:

Genes affected

SPATA7 (HGNC:20423): (spermatogenesis associated 7) This gene, originally isolated from testis, is also expressed in retina. Mutations in this gene are associated with Leber congenital amaurosis and juvenile retinitis pigmentosa. Alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, May 2010]

SPATA7 links:

SPATA7 (HGNC:):

SPATA7 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.55).

BP6

Variant 14-88391362-T-G is Benign according to our data. Variant chr14-88391362-T-G is described in ClinVar as [Benign]. Clinvar id is 1170459.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0995 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SPATA7	NM_018418.5 linkuse as main transcript	c.20-19T>G		intron_variant		ENST00000393545.9	NP_060888.2	Q9P0W8-1V9HVY9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SPATA7	ENST00000393545.9 linkuse as main transcript	c.20-19T>G		intron_variant		1	NM_018418.5	ENSP00000377176.4		Q9P0W8-1

Frequencies

GnomAD3 genomes

AF:

0.0674

AC:

10242

AN:

152024

Hom.:

498

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0177

Gnomad AMI

AF:

0.0515

Gnomad AMR

AF:

0.0577

Gnomad ASJ

AF:

0.0934

Gnomad EAS

AF:

0.000578

Gnomad SAS

AF:

0.0211

Gnomad FIN

AF:

0.102

Gnomad MID

AF:

0.0728

Gnomad NFE

AF:

0.101

Gnomad OTH

AF:

0.0724

GnomAD3 exomes

AF:

0.0707

AC:

17460

AN:

247078

Hom.:

821

AF XY:

0.0719

AC XY:

9622

AN XY:

133788

show subpopulations

Gnomad AFR exome

AF:

0.0159

Gnomad AMR exome

AF:

0.0477

Gnomad ASJ exome

AF:

0.0979

Gnomad EAS exome

AF:

0.000110

Gnomad SAS exome

AF:

0.0201

Gnomad FIN exome

AF:

0.105

Gnomad NFE exome

AF:

0.101

Gnomad OTH exome

AF:

0.0838

GnomAD4 exome

AF:

0.0868

AC:

125753

AN:

1449236

Hom.:

6199

Cov.:

AF XY:

0.0853

AC XY:

61570

AN XY:

721538

show subpopulations

Gnomad4 AFR exome

AF:

0.0132

Gnomad4 AMR exome

AF:

0.0489

Gnomad4 ASJ exome

AF:

0.0971

Gnomad4 EAS exome

AF:

0.000228

Gnomad4 SAS exome

AF:

0.0214

Gnomad4 FIN exome

AF:

0.104

Gnomad4 NFE exome

AF:

0.0981

Gnomad4 OTH exome

AF:

0.0800

GnomAD4 genome

AF:

0.0673

AC:

10237

AN:

152142

Hom.:

499

Cov.:

AF XY:

0.0657

AC XY:

4884

AN XY:

74390

show subpopulations

Gnomad4 AFR

AF:

0.0177

Gnomad4 AMR

AF:

0.0575

Gnomad4 ASJ

AF:

0.0934

Gnomad4 EAS

AF:

0.000579

Gnomad4 SAS

AF:

0.0213

Gnomad4 FIN

AF:

0.102

Gnomad4 NFE

AF:

0.101

Gnomad4 OTH

AF:

0.0707

Alfa

AF:

0.0903

Hom.:

127

Bravo

AF:

0.0608

Asia WGS

AF:

0.0120

AC:

AN:

3476

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

Leber congenital amaurosis 3

Benign:1

Benign, criteria provided, single submitter

clinical testing

Labcorp Genetics (formerly Invitae), Labcorp

Jan 31, 2024

- -

not provided

Benign:1

Benign, criteria provided, single submitter

not provided

Breakthrough Genomics, Breakthrough Genomics

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.55

CADD

Benign

8.6

DANN

Benign

0.78

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.050

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