Variant 17-4960115-A-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_004890.3(SPAG7):c.328-4T>C variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.821 in 1,612,340 control chromosomes in the GnomAD database, including 550,499 homozygotes. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.82 ( 51477 hom., cov: 34)

Exomes 𝑓: 0.82 ( 499022 hom. )

Consequence

SPAG7
NM_004890.3 splice_region, intron

Scores

Splicing: ADA: 0.000009876

Clinical Significance

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

Conservation

PhyloP100: -0.0820

Variant links:

Genes affected

SPAG7 (HGNC:11216): (sperm associated antigen 7) Predicted to enable nucleic acid binding activity. Predicted to be located in nucleus. [provided by Alliance of Genome Resources, Apr 2022]

SPAG7 links:

SPAG7 (HGNC:):

SPAG7 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=-0.82).

BP6

Variant 17-4960115-A-G is Benign according to our data. Variant chr17-4960115-A-G is described in ClinVar as [Benign]. Clinvar id is 403467.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.844 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SPAG7	NM_004890.3 linkuse as main transcript	c.328-4T>C		splice_region_variant, intron_variant		ENST00000206020.8	NP_004881.2	O75391

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SPAG7	ENST00000206020.8 linkuse as main transcript	c.328-4T>C		splice_region_variant, intron_variant		1	NM_004890.3	ENSP00000206020.3		O75391

Frequencies

GnomAD3 genomes

AF:

0.818

AC:

124377

AN:

152100

Hom.:

51415

Cov.:

show subpopulations

Gnomad AFR

AF:

0.834

Gnomad AMI

AF:

0.810

Gnomad AMR

AF:

0.842

Gnomad ASJ

AF:

0.860

Gnomad EAS

AF:

0.455

Gnomad SAS

AF:

0.575

Gnomad FIN

AF:

0.783

Gnomad MID

AF:

0.892

Gnomad NFE

AF:

0.849

Gnomad OTH

AF:

0.853

GnomAD3 exomes

AF:

0.782

AC:

195064

AN:

249480

Hom.:

78322

AF XY:

0.776

AC XY:

105003

AN XY:

135360

show subpopulations

Gnomad AFR exome

AF:

0.837

Gnomad AMR exome

AF:

0.822

Gnomad ASJ exome

AF:

0.859

Gnomad EAS exome

AF:

0.460

Gnomad SAS exome

AF:

0.586

Gnomad FIN exome

AF:

0.788

Gnomad NFE exome

AF:

0.856

Gnomad OTH exome

AF:

0.820

GnomAD4 exome

AF:

0.822

AC:

1199848

AN:

1460122

Hom.:

499022

Cov.:

AF XY:

0.816

AC XY:

592880

AN XY:

726534

show subpopulations

Gnomad4 AFR exome

AF:

0.836

Gnomad4 AMR exome

AF:

0.825

Gnomad4 ASJ exome

AF:

0.861

Gnomad4 EAS exome

AF:

0.466

Gnomad4 SAS exome

AF:

0.599

Gnomad4 FIN exome

AF:

0.797

Gnomad4 NFE exome

AF:

0.852

Gnomad4 OTH exome

AF:

0.808

GnomAD4 genome

AF:

0.818

AC:

124496

AN:

152218

Hom.:

51477

Cov.:

AF XY:

0.809

AC XY:

60259

AN XY:

74440

show subpopulations

Gnomad4 AFR

AF:

0.834

Gnomad4 AMR

AF:

0.842

Gnomad4 ASJ

AF:

0.860

Gnomad4 EAS

AF:

0.455

Gnomad4 SAS

AF:

0.576

Gnomad4 FIN

AF:

0.783

Gnomad4 NFE

AF:

0.849

Gnomad4 OTH

AF:

0.851

Alfa

AF:

0.845

Hom.:

87068

Bravo

AF:

0.826

Asia WGS

AF:

0.560

AC:

1952

AN:

3478

EpiCase

AF:

0.847

EpiControl

AF:

0.858

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not specified

Benign:1

Benign, criteria provided, single submitter

clinical testing

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

Mar 29, 2016

Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or databases. Disclaimer: This variant has not undergone full assessment. The following are preliminary notes: Frequency -

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

-0.82

CADD

Benign

3.8

DANN

Benign

0.63

Splicing

Name

Calibrated prediction

Score

Prediction

dbscSNV1_ADA

Benign

0.0000099

dbscSNV1_RF

Benign

0.0

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