15-45402570-G-T

Variant summary

Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_Strong BP6_Moderate BP7 BA1

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
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.994

Genes affected

SPATA5L1 (HGNC:):

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]

ACMG classification

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
SPATA5L1	NM_024063.3	c.141G>T	p.Val47=	synonymous_variant	1/8	ENST00000305560.11

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.119 AC: 18132 AN: 152126 Hom.: 3617 Cov.: 33

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

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

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

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

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Jun 26, 2018

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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

Other links and lift over

dbSNP: rs1834686; hg19: chr15-45694768;