rs769395407

Variant names:

• chr9-81947502-C-G
• rs769395407
• NM_207416.3:c.2249C>G

Your query was ambiguous. Multiple possible variants found:

• chr9-81947502-C-G
• chr9-81947502-C-T

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 0P and 2B. BP4_Moderate

The NM_207416.3(SPATA31D3):​c.2249C>G​(p.Pro750Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. 9/12 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: not found (cov: 19)
  • Exomes 𝑓: 7.3e-7 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: SPATA31D3 NM_207416.3 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.551

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

Verdict is Likely_benign. Variant got -2 ACMG points.

• BP4: Computational evidence support a benign effect (MetaRNN=0.17024535).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SPATA31D3	NM_207416.3	c.2249C>G	p.Pro750Arg	missense_variant	Exon 4 of 4	ENST00000445385.3	NP_997299.2
LOC105376105	NR_188610.1	n.943-1016G>C		intron_variant	Intron 3 of 5
LOC105376105	NR_188611.1	n.943-1016G>C		intron_variant	Intron 3 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SPATA31D3	ENST00000445385.3	c.2249C>G	p.Pro750Arg	missense_variant	Exon 4 of 4	1	NM_207416.3	ENSP00000488117.1
ENSG00000267559	ENST00000585776.5	n.943-1016G>C		intron_variant	Intron 3 of 4	2
ENSG00000267559	ENST00000592744.1	n.519-1016G>C		intron_variant	Intron 3 of 3	4

Frequencies

GnomAD3 genomes Cov.: 19

GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 7.31e-7 AC: 1 AN: 1367068 Hom.: 0 Cov.: 28 AF XY: 0.00 AC XY: 0 AN XY: 677954

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 9.55e-7

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Cov.: 19

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.11
BayesDel_noAF	Benign	-0.90
CADD	Benign	11
DANN	Benign	0.36
DEOGEN2	Benign	0.021	T
FATHMM_MKL	Benign	0.0091	N
LIST_S2	Benign	0.38	T
MetaRNN	Benign	0.17	T
MutationAssessor	Benign	1.8	L
PrimateAI	Benign	0.35	T
Sift4G	Uncertain	0.012	D
Polyphen		0.91	P
Vest4		0.12
GERP RS		1.2
Varity_R		0.033
gMVP		0.062

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: rs769395407; hg19: chr9-84562417;