rs190034

Variant names:

• chr5-95681827-C-T
• rs190034
• NM_031952.4:c.150+701G>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 5 publications found

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]

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]

LOC105379090 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
SPATA9	NM_031952.4	c.150+701G>A		intron_variant	Intron 2 of 4	ENST00000274432.13	NP_114158.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SPATA9	ENST00000274432.13	c.150+701G>A		intron_variant	Intron 2 of 4	1	NM_031952.4	ENSP00000274432.8

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

African (AFR) AF: 0.331 AC: 13714 AN: 41432

American (AMR) AF: 0.323 AC: 4934 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.321 AC: 1113 AN: 3466

East Asian (EAS) AF: 0.240 AC: 1241 AN: 5168

South Asian (SAS) AF: 0.391 AC: 1885 AN: 4824

European-Finnish (FIN) AF: 0.484 AC: 5112 AN: 10558

Middle Eastern (MID) AF: 0.313 AC: 92 AN: 294

European-Non Finnish (NFE) AF: 0.411 AC: 27924 AN: 67934

Other (OTH) AF: 0.377 AC: 793 AN: 2106

Alfa AF: 0.382 Hom.: 2220

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
PhyloP100		-0.022
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs190034; hg19: chr5-95017531;