rs6750230

Positions:

• chr2-231015397-G-A
• chr2-231015397-G-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000452881.5(SPATA3):​c.*565+1185G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.399 in 151,546 control chromosomes in the GnomAD database, including 12,943 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 0.40 (12943 hom., cov: 30)
• Consequence: SPATA3 ENST00000452881.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.830

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.54 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SPATA3	XM_017003363.3	c.*39-4323G>A		intron_variant
SPATA3	XM_047443398.1	c.*29-4323G>A		intron_variant
SPATA3	XR_001738624.3	n.811-4323G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SPATA3	ENST00000452881.5	c.*565+1185G>A		intron_variant		2		P1
SPATA3	ENST00000455816.1	c.*146+2700G>A		intron_variant		5		P1
SPATA3	ENST00000495639.1	c.*39-4323G>A		intron_variant		3

Frequencies

GnomAD3 genomes AF: 0.399 AC: 60350 AN: 151428 Hom.: 12912 Cov.: 30

Gnomad AFR AF: 0.546

Gnomad AMI AF: 0.364

Gnomad AMR AF: 0.448

Gnomad ASJ AF: 0.242

Gnomad EAS AF: 0.342

Gnomad SAS AF: 0.300

Gnomad FIN AF: 0.356

Gnomad MID AF: 0.404

Gnomad NFE AF: 0.325

Gnomad OTH AF: 0.380

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

GnomAD4 genome AF: 0.399 AC: 60424 AN: 151546 Hom.: 12943 Cov.: 30 AF XY: 0.398 AC XY: 29475 AN XY: 73992

Gnomad4 AFR AF: 0.546

Gnomad4 AMR AF: 0.449

Gnomad4 ASJ AF: 0.242

Gnomad4 EAS AF: 0.343

Gnomad4 SAS AF: 0.299

Gnomad4 FIN AF: 0.356

Gnomad4 NFE AF: 0.325

Gnomad4 OTH AF: 0.378

Alfa AF: 0.320 Hom.: 4039

Bravo AF: 0.415

Asia WGS AF: 0.358 AC: 1243 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.6
DANN	Benign	0.70

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs6750230; hg19: chr2-231880112;