dbSNP rs10192428: SPATA3:c.*378G>A (chr2-231014025-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000452881.5(SPATA3):c.*378G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.437 in 151,604 control chromosomes in the GnomAD database, including 15,572 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 0.44 ( 15572 hom., cov: 29)

Exomes 𝑓: 0.50 ( 0 hom. )

Consequence

SPATA3
ENST00000452881.5 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.586

Variant links:

Genes affected

SPATA3 (HGNC:17884): (spermatogenesis associated 3) Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]

SPATA3 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=-0.87).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.587 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank	Protein	UniProt
SPATA3	XM_047443398.1 link	c.*29-5695G>A	intron_variant	Intron 3 of 3	XP_047299354.1
SPATA3	XM_017003363.3 link	c.*39-5695G>A	intron_variant	Intron 3 of 3	XP_016858852.1	Q8NHX4
SPATA3	XR_001738627.3 link	n.1070G>A	non_coding_transcript_exon_variant	Exon 6 of 6

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	Protein	UniProt
SPATA3	ENST00000452881.5 link	c.*378G>A	3_prime_UTR_variant	Exon 6 of 9	2	ENSP00000388895.1	Q8NHX4
SPATA3	ENST00000455816.1 link	c.*146+1328G>A	intron_variant	Intron 4 of 4	5	ENSP00000388741.1	Q8NHX4
SPATA3	ENST00000495639.1 link	c.*39-5695G>A	intron_variant	Intron 1 of 3	3	ENSP00000436378.1

Frequencies

GnomAD3 genomes

AF:

0.436

AC:

66104

AN:

151482

Hom.:

15540

Cov.:

show subpopulations

Gnomad AFR

AF:

0.594

Gnomad AMI

AF:

0.434

Gnomad AMR

AF:

0.495

Gnomad ASJ

AF:

0.252

Gnomad EAS

AF:

0.474

Gnomad SAS

AF:

0.485

Gnomad FIN

AF:

0.378

Gnomad MID

AF:

0.427

Gnomad NFE

AF:

0.341

Gnomad OTH

AF:

0.415

GnomAD4 exome

AF:

0.500

AC:

AN:

Hom.:

Cov.:

AF XY:

0.500

AC XY:

AN XY:

show subpopulations

Gnomad4 FIN exome

AF:

0.500

GnomAD4 genome

AF:

0.437

AC:

66189

AN:

151600

Hom.:

15572

Cov.:

AF XY:

0.439

AC XY:

32527

AN XY:

74072

show subpopulations

Gnomad4 AFR

AF:

0.594

Gnomad4 AMR

AF:

0.496

Gnomad4 ASJ

AF:

0.252

Gnomad4 EAS

AF:

0.475

Gnomad4 SAS

AF:

0.483

Gnomad4 FIN

AF:

0.378

Gnomad4 NFE

AF:

0.341

Gnomad4 OTH

AF:

0.414

Alfa

AF:

0.414

Hom.:

2850

Bravo

AF:

0.451

Asia WGS

AF:

0.543

AC:

1887

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.87

CADD

Benign

3.8

DANN

Benign

0.75

Splicing

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