rs1462222560

Variant names:

• chr9-81947580-C-A
• rs1462222560
• NM_207416.3:c.2327C>A

Your query was ambiguous. Multiple possible variants found:

• chr9-81947580-C-A
• chr9-81947580-C-G
• chr9-81947580-C-T

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_207416.3(SPATA31D3):​c.2327C>A​(p.Thr776Asn) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: 22)
• Consequence: SPATA31D3 NM_207416.3 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.605

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.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.0367288).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SPATA31D3	NM_207416.3	c.2327C>A	p.Thr776Asn	missense_variant	Exon 4 of 4	ENST00000445385.3	NP_997299.2
LOC105376105	NR_188610.1	n.943-1094G>T		intron_variant	Intron 3 of 5
LOC105376105	NR_188611.1	n.943-1094G>T		intron_variant	Intron 3 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SPATA31D3	ENST00000445385.3	c.2327C>A	p.Thr776Asn	missense_variant	Exon 4 of 4	1	NM_207416.3	ENSP00000488117.1
ENSG00000267559	ENST00000585776.5	n.943-1094G>T		intron_variant	Intron 3 of 4	2
ENSG00000267559	ENST00000592744.1	n.519-1094G>T		intron_variant	Intron 3 of 3	4

Frequencies

GnomAD3 genomes Cov.: 22

GnomAD3 exomes AF: 0.00000440 AC: 1 AN: 227282 Hom.: 0 AF XY: 0.00 AC XY: 0 AN XY: 123636

Gnomad AFR exome AF: 0.00

Gnomad AMR exome AF: 0.00

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.00

Gnomad SAS exome AF: 0.00

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.00000967

Gnomad OTH exome AF: 0.00

GnomAD4 exome Cov.: 31

GnomAD4 genome Cov.: 22

Alfa AF: 0.0000435 Hom.: 0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.060
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.0020
DANN	Benign	0.48
DEOGEN2	Benign	0.0012	T
FATHMM_MKL	Benign	0.00020	N
LIST_S2	Benign	0.31	T
MetaRNN	Benign	0.037	T
MutationAssessor	Benign	-0.73	N
PrimateAI	Benign	0.45	T
Sift4G	Benign	1.0	T
Polyphen		0.0	B
Vest4		0.063
GERP RS		-4.0
Varity_R		0.034
gMVP		0.030

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: rs1462222560; hg19: chr9-84562495;