Variant 15-45406595-T-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_024063.3(SPATA5L1):c.1275+1090T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.561 in 152,044 control chromosomes in the GnomAD database, including 27,396 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.56 ( 27396 hom., cov: 32)

Consequence

SPATA5L1
NM_024063.3 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.480

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 -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.98).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.886 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SPATA5L1	NM_024063.3 linkuse as main transcript	c.1275+1090T>G		intron_variant		ENST00000305560.11

Ensembl

Gene	Transcript	HGVSc	Effect	TSL	MANE	Appris	UniProt
AFG2B	ENST00000305560.11 linkuse as main transcript	c.1275+1090T>G	intron_variant	1	NM_024063.3	P1	Q9BVQ7-1
AFG2B	ENST00000525552.1 linkuse as main transcript	c.48-434T>G	intron_variant, NMD_transcript_variant	3
AFG2B	ENST00000531970.5 linkuse as main transcript	c.1275+1090T>G	intron_variant, NMD_transcript_variant	2			Q9BVQ7-2
AFG2B	ENST00000559860.2 linkuse as main transcript	n.1335+1090T>G	intron_variant, non_coding_transcript_variant	2

Frequencies

GnomAD3 genomes

AF:

0.560

AC:

85151

AN:

151926

Hom.:

27337

Cov.:

show subpopulations

Gnomad AFR

AF:

0.842

Gnomad AMI

AF:

0.234

Gnomad AMR

AF:

0.620

Gnomad ASJ

AF:

0.533

Gnomad EAS

AF:

0.908

Gnomad SAS

AF:

0.595

Gnomad FIN

AF:

0.408

Gnomad MID

AF:

0.551

Gnomad NFE

AF:

0.377

Gnomad OTH

AF:

0.557

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome

AF:

0.561

AC:

85274

AN:

152044

Hom.:

27396

Cov.:

AF XY:

0.567

AC XY:

42159

AN XY:

74304

show subpopulations

Gnomad4 AFR

AF:

0.842

Gnomad4 AMR

AF:

0.620

Gnomad4 ASJ

AF:

0.533

Gnomad4 EAS

AF:

0.908

Gnomad4 SAS

AF:

0.593

Gnomad4 FIN

AF:

0.408

Gnomad4 NFE

AF:

0.377

Gnomad4 OTH

AF:

0.562

Alfa

AF:

0.413

Hom.:

5928

Bravo

AF:

0.592

Asia WGS

AF:

0.737

AC:

2548

AN:

3460

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.98

CADD

Benign

6.7

DANN

Benign

0.77

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

Computational scores

Splicing

Publications

LitVar

Other links and lift over