chr15-45402570-G-T

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

2

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.994
Variant links:
Genes affected
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]

Genome browser will be placed here

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 UniProt
SPATA5L1NM_024063.3 linkuse as main transcriptc.141G>T p.Val47= synonymous_variant 1/8 ENST00000305560.11

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
AFG2BENST00000305560.11 linkuse as main transcriptc.141G>T p.Val47= synonymous_variant 1/81 NM_024063.3 P1Q9BVQ7-1
AFG2BENST00000559860.2 linkuse as main transcriptn.201G>T non_coding_transcript_exon_variant 1/52
AFG2BENST00000531970.5 linkuse as main transcriptc.141G>T p.Val47= synonymous_variant, NMD_transcript_variant 1/82 Q9BVQ7-2

Frequencies

GnomAD3 genomes
AF:
0.119
AC:
18132
AN:
152126
Hom.:
3617
Cov.:
33
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.:
33
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.:
33
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 submitterclinical testingGeneDxJun 26, 2018- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.48
CADD
Benign
12
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.

Other links and lift over

dbSNP: rs1834686; hg19: chr15-45694768; API