rs190034

chr5-95681827-C-T

Variant summary

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

The NM_031952.4(SPATA9):c.150+701G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.377 in 151,962 control chromosomes in the GnomAD database, including 10,959 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 0.38 (10959 hom., cov: 32)
• Consequence: SPATA9 NM_031952.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0220

Genes affected

SPATA9 (HGNC:22988): (spermatogenesis associated 9) Predicted to be involved in cell differentiation and spermatogenesis. Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]

LOC105379090 (HGNC:):

RFESD (HGNC:29587): (Rieske Fe-S domain containing) Predicted to enable 2 iron, 2 sulfur cluster binding activity and metal ion binding activity. [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=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.407 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SPATA9	NM_031952.4	c.150+701G>A		intron_variant		ENST00000274432.13
LOC105379090	XR_948588.3	n.161-2768C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SPATA9	ENST00000274432.13	c.150+701G>A		intron_variant		1	NM_031952.4	P1

Frequencies

GnomAD3 genomes AF: 0.377 AC: 57257 AN: 151844 Hom.: 10946 Cov.: 32

Gnomad AFR AF: 0.332

Gnomad AMI AF: 0.536

Gnomad AMR AF: 0.324

Gnomad ASJ AF: 0.321

Gnomad EAS AF: 0.239

Gnomad SAS AF: 0.390

Gnomad FIN AF: 0.484

Gnomad MID AF: 0.291

Gnomad NFE AF: 0.411

Gnomad OTH AF: 0.369

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

GnomAD4 genome AF: 0.377 AC: 57295 AN: 151962 Hom.: 10959 Cov.: 32 AF XY: 0.379 AC XY: 28174 AN XY: 74272

Gnomad4 AFR AF: 0.331

Gnomad4 AMR AF: 0.323

Gnomad4 ASJ AF: 0.321

Gnomad4 EAS AF: 0.240

Gnomad4 SAS AF: 0.391

Gnomad4 FIN AF: 0.484

Gnomad4 NFE AF: 0.411

Gnomad4 OTH AF: 0.377

Alfa AF: 0.383 Hom.: 2169

Bravo AF: 0.364

Asia WGS AF: 0.322 AC: 1118 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	1.4
Dann	Benign	0.67

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: rs190034; hg19: chr5-95017531;