Variant chr15-45402570-G-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BA1

The NM_024063.3(SPATA5L1):c.141G>T(p.Val47=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0245 in 1,579,392 control chromosomes in the GnomAD database, including 6,954 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.12 ( 3644 hom., cov: 33)

Exomes 𝑓: 0.014 ( 3310 hom. )

Consequence

SPATA5L1
NM_024063.3 synonymous

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.994

Variant links:

Genes affected

SPATA5L1 (HGNC:):

SPATA5L1 links:

AFG2B (HGNC:28762): (AFG2 AAA ATPase homolog B) Predicted to enable ATP binding activity. Located in cytoplasm and spindle. [provided by Alliance of Genome Resources, Apr 2022]

AFG2B links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -15 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.48).

BP6

Variant 15-45402570-G-T is Benign according to our data. Variant chr15-45402570-G-T is described in ClinVar as [Benign]. Clinvar id is 1235297.Status of the report is criteria_provided_single_submitter, 1 stars.

BP7

Synonymous conserved (PhyloP=0.994 with no splicing effect.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.409 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SPATA5L1	NM_024063.3 linkuse as main transcript	c.141G>T	p.Val47=	synonymous_variant	1/8	ENST00000305560.11	NP_076968.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
AFG2B	ENST00000305560.11 linkuse as main transcript	c.141G>T	p.Val47=	synonymous_variant	1/8	1	NM_024063.3	ENSP00000305494	P1	Q9BVQ7-1
AFG2B	ENST00000559860.2 linkuse as main transcript	n.201G>T		non_coding_transcript_exon_variant	1/5	2
AFG2B	ENST00000531970.5 linkuse as main transcript	c.141G>T	p.Val47=	synonymous_variant, NMD_transcript_variant	1/8	2		ENSP00000436823		Q9BVQ7-2

Frequencies

GnomAD3 genomes

AF:

0.119

AC:

18132

AN:

152126

Hom.:

3617

Cov.:

show subpopulations

Gnomad AFR

AF:

0.414

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0332

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00289

Gnomad SAS

AF:

0.0488

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.0127

Gnomad NFE

AF:

0.00113

Gnomad OTH

AF:

0.0817

GnomAD3 exomes

AF:

0.0316

AC:

5759

AN:

182076

Hom.:

938

AF XY:

0.0278

AC XY:

2780

AN XY:

100156

show subpopulations

Gnomad AFR exome

AF:

0.432

Gnomad AMR exome

AF:

0.0129

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.00180

Gnomad SAS exome

AF:

0.0429

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.000590

Gnomad OTH exome

AF:

0.0132

GnomAD4 exome

AF:

0.0144

AC:

20546

AN:

1427148

Hom.:

3310

Cov.:

AF XY:

0.0139

AC XY:

9859

AN XY:

707752

show subpopulations

Gnomad4 AFR exome

AF:

0.432

Gnomad4 AMR exome

AF:

0.0164

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.000996

Gnomad4 SAS exome

AF:

0.0424

Gnomad4 FIN exome

AF:

0.00

Gnomad4 NFE exome

AF:

0.000439

Gnomad4 OTH exome

AF:

0.0299

GnomAD4 genome

AF:

0.120

AC:

18202

AN:

152244

Hom.:

3644

Cov.:

AF XY:

0.115

AC XY:

8598

AN XY:

74448

show subpopulations

Gnomad4 AFR

AF:

0.414

Gnomad4 AMR

AF:

0.0329

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.00251

Gnomad4 SAS

AF:

0.0488

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.00113

Gnomad4 OTH

AF:

0.0847

Alfa

AF:

0.0272

Hom.:

296

Bravo

AF:

0.134

Asia WGS

AF:

0.0580

AC:

201

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Jun 26, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.48

CADD

Benign

DANN

Benign

0.85

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