9-61192933-T-A

Variant names:

• chr9-61192933-T-A
• NM_015667.2:c.847T>A

Variant summary

Our verdict is Likely benign. The variant received -1 ACMG points: 0P and 1B. BP4

The NM_015667.2(SPATA31A7):​c.847T>A​(p.Trp283Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. 6/9 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. W283C) has been classified as Uncertain significance.

• Frequency: Genomes: not found (cov: 5)
• Consequence: SPATA31A7 NM_015667.2 missense
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: 1.75
• Publications: 0 publications found

Genes affected

SPATA31A7 (HGNC:32007): (SPATA31 subfamily A member 7) Predicted to be involved in cell differentiation and spermatogenesis. Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Likely_benign. The variant received -1 ACMG points.

• BP4: Computational evidence support a benign effect (MetaRNN=0.28878927).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_015667.2. 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
	SPATA31A7	NM_015667.2	MANE Select	c.847T>A	p.Trp283Arg	missense	Exon 4 of 4	NP_056482.2	Q8IWB4

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SPATA31A7	ENST00000619167.2	TSL:1 MANE Select	c.847T>A	p.Trp283Arg	missense	Exon 4 of 4	ENSP00000484807.1	Q8IWB4
	SPATA31A7	ENST00000618860.4	TSL:5	n.698T>A		non_coding_transcript_exon	Exon 3 of 3
	SPATA31A7	ENST00000621711.1	TSL:5	n.234+477T>A		intron	N/A

Frequencies

GnomAD3 genomes Cov.: 5

GnomAD4 exome Cov.: 14

GnomAD4 genome Cov.: 5

ClinVar

ClinVar submissions

Significance: Uncertain significance

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	Uncertain	0.42
BayesDel_noAF	Benign	-0.25
CADD	Benign	21
DANN	Benign	0.95
DEOGEN2	Benign	0.19	T
LIST_S2	Benign	0.33	T
MetaRNN	Benign	0.29	T
PhyloP100		1.7
Sift4G	Uncertain	0.010	D
Vest4		0.34
gMVP		0.28

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

hg19: chr9-43627840;