9-35045566-C-A

Variant names:

• chr9-35045566-C-A
• rs1394906030
• NM_203299.4:c.2937C>A

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 2P and 6B. PM2 BP4_Strong BP6_Moderate

The NM_203299.4(SPATA31G1):​c.2937C>A​(p.Ser979Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000752 in 1,461,878 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

• Frequency:
  • Genomes: not found (cov: 32)
  • Exomes 𝑓: 0.0000075 (0 hom.)
• Consequence: SPATA31G1 NM_203299.4 missense
• Clinical Significance: Likely benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.309
• Publications: 0 publications found

Genes affected

SPATA31G1 (HGNC:31418): (SPATA31 subfamily G member 1)

ACMG classification

Our verdict: Likely_benign. The variant received -4 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.019129425).
• BP6: Variant 9-35045566-C-A is Benign according to our data. Variant chr9-35045566-C-A is described in ClinVar as Likely_benign. ClinVar VariationId is 2237994.Status of the report is criteria_provided_single_submitter, 1 stars.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_203299.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SPATA31G1	NM_203299.4	MANE Select	c.2937C>A	p.Ser979Arg	missense	Exon 2 of 2	NP_976044.2	Q5VYM1-1
	SPATA31G1	NM_001040410.3		c.2832C>A	p.Ser944Arg	missense	Exon 2 of 2	NP_001035500.1
	SPATA31G1	NM_001040412.3		c.2793C>A	p.Ser931Arg	missense	Exon 3 of 3	NP_001035502.1	Q5VYM1-2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SPATA31G1	ENST00000312292.6	TSL:1 MANE Select	c.2937C>A	p.Ser979Arg	missense	Exon 2 of 2	ENSP00000308279.5	Q5VYM1-1
	SPATA31G1	ENST00000421362.6	TSL:4	c.2793C>A	p.Ser931Arg	missense	Exon 3 of 3	ENSP00000393683.2	Q5VYM1-2
	SPATA31G1	ENST00000354479.5	TSL:2	c.2718C>A	p.Ser906Arg	missense	Exon 2 of 2	ENSP00000346472.5	Q5VYM1-3

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome AF: 0.00000752 AC: 11 AN: 1461878 Hom.: 0 Cov.: 34 AF XY: 0.00000688 AC XY: 5 AN XY: 727242

African (AFR) AF: 0.00 AC: 0 AN: 33480

American (AMR) AF: 0.00 AC: 0 AN: 44724

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 26136

East Asian (EAS) AF: 0.00 AC: 0 AN: 39700

South Asian (SAS) AF: 0.00 AC: 0 AN: 86258

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 53406

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 5768

European-Non Finnish (NFE) AF: 0.00000989 AC: 11 AN: 1112010

Other (OTH) AF: 0.00 AC: 0 AN: 60396

GnomAD4 genome Cov.: 32

Alfa AF: 0.0000712 Hom.: 0

Bravo AF: 0.00000378

ClinVar

ClinVar submissions

Significance: Likely benign

Revision: criteria provided, single submitter

Pathogenic	VUS	Benign	Condition
-	-	1	not specified (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.19
BayesDel_addAF	Benign	-0.38	T
BayesDel_noAF	Benign	-0.78
CADD	Benign	0.18
DANN	Benign	0.59
DEOGEN2	Benign	0.0014	T
Eigen	Benign	-1.8
Eigen_PC	Benign	-1.7
FATHMM_MKL	Benign	0.0025	N
LIST_S2	Benign	0.60	T
M_CAP	Benign	0.0017	T
MetaRNN	Benign	0.019	T
MetaSVM	Benign	-0.95	T
MutationAssessor	Benign	-2.1	N
PhyloP100		0.31
PROVEAN	Benign	2.8	N
REVEL	Benign	0.023
Sift	Benign	1.0	T
Sift4G	Benign	1.0	T
Polyphen		0.0	B
Vest4		0.085
MutPred		0.20		Gain of MoRF binding (P = 0.0172)
MVP		0.014
MPC		0.012
ClinPred		0.094	T
GERP RS		-1.7
Varity_R		0.045
gMVP		0.070
Mutation Taster		=99/1	polymorphism

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: rs1394906030; hg19: chr9-35045563;