9-81945220-C-T

Variant names:

• chr9-81945220-C-T
• rs767047424
• NM_207416.3:c.281C>T

Variant summary

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

The NM_207416.3(SPATA31D3):​c.281C>T​(p.Ser94Phe) variant causes a missense change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. 8/12 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. S94Y) has been classified as Uncertain significance.

• Frequency:
  • Genomes: 𝑓 0.0 (0 hom., cov: 9)
  • Failed GnomAD Quality Control
• Consequence: SPATA31D3 NM_207416.3 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0550
• Publications: 1 publications found

Genes affected

SPATA31D3 (HGNC:38603): (SPATA31 subfamily D member 3) Predicted to be involved in cell differentiation and spermatogenesis. Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]

ENSG00000267559 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (MetaRNN=0.36581868).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_207416.3. 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
	SPATA31D3	NM_207416.3	MANE Select	c.281C>T	p.Ser94Phe	missense	Exon 3 of 4	NP_997299.2	P0C874
	LOC105376105	NR_188610.1		n.1039+1170G>A		intron	N/A
	LOC105376105	NR_188611.1		n.1228+981G>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SPATA31D3	ENST00000445385.3	TSL:1 MANE Select	c.281C>T	p.Ser94Phe	missense	Exon 3 of 4	ENSP00000488117.1	P0C874
	ENSG00000267559	ENST00000585776.5	TSL:2	n.1039+1170G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.00 AC: 0 AN: 57000 Hom.: 0 Cov.: 9

Gnomad AFR AF: 0.00

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00

Gnomad OTH AF: 0.00

GnomAD4 exome Cov.: 15

GnomAD4 genome Data not reliable, filtered out with message: AC0;AS_VQSR AF: 0.00 AC: 0 AN: 57000 Hom.: 0 Cov.: 9 AF XY: 0.00 AC XY: 0 AN XY: 25604

African (AFR) AF: 0.00 AC: 0 AN: 14076

American (AMR) AF: 0.00 AC: 0 AN: 3366

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 1888

East Asian (EAS) AF: 0.00 AC: 0 AN: 1900

South Asian (SAS) AF: 0.00 AC: 0 AN: 1334

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 672

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 56

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 32584

Other (OTH) AF: 0.00 AC: 0 AN: 702

Alfa AF: 0.00 Hom.: 0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.13
BayesDel_noAF	Benign	-0.92
CADD	Benign	18
DANN	Benign	0.53
DEOGEN2	Benign	0.19	T
FATHMM_MKL	Benign	0.0097	N
LIST_S2	Benign	0.61	T
MetaRNN	Benign	0.37	T
MutationAssessor	Uncertain	2.4	M
PhyloP100		-0.055
PrimateAI	Benign	0.48	T
Sift4G	Uncertain	0.0040	D
Polyphen		0.95	P
Vest4		0.37
GERP RS		-0.90
Varity_R		0.086
gMVP		0.057
Mutation Taster		=100/0	polymorphism

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.050		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: rs767047424; hg19: chr9-84560135;