rs1878007

Positions:

• chr3-173081010-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_031955.6(SPATA16):​c.613-31916C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.14 in 152,094 control chromosomes in the GnomAD database, including 1,889 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.14 (1889 hom., cov: 32)
• Consequence: SPATA16 NM_031955.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0530

Genes affected

SPATA16 (HGNC:29935): (spermatogenesis associated 16) This gene encodes a testis-specific protein that belongs to the tetratricopeptide repeat-like superfamily. The encoded protein localizes to the Golgi apparatus and may play a role in spermatogenesis. [provided by RefSeq, May 2010]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.271 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SPATA16	NM_031955.6	c.613-31916C>T		intron_variant		ENST00000351008.4	NP_114161.3
SPATA16	XM_006713778.4	c.613-31916C>T		intron_variant			XP_006713841.1
SPATA16	XM_017007308.3	c.613-31916C>T		intron_variant			XP_016862797.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SPATA16	ENST00000351008.4	c.613-31916C>T		intron_variant		1	NM_031955.6	ENSP00000341765	P1

Frequencies

GnomAD3 genomes AF: 0.140 AC: 21324 AN: 151976 Hom.: 1889 Cov.: 32

Gnomad AFR AF: 0.0369

Gnomad AMI AF: 0.114

Gnomad AMR AF: 0.156

Gnomad ASJ AF: 0.170

Gnomad EAS AF: 0.178

Gnomad SAS AF: 0.285

Gnomad FIN AF: 0.218

Gnomad MID AF: 0.156

Gnomad NFE AF: 0.173

Gnomad OTH AF: 0.154

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.140 AC: 21319 AN: 152094 Hom.: 1889 Cov.: 32 AF XY: 0.145 AC XY: 10767 AN XY: 74342

Gnomad4 AFR AF: 0.0368

Gnomad4 AMR AF: 0.156

Gnomad4 ASJ AF: 0.170

Gnomad4 EAS AF: 0.179

Gnomad4 SAS AF: 0.284

Gnomad4 FIN AF: 0.218

Gnomad4 NFE AF: 0.173

Gnomad4 OTH AF: 0.152

Alfa AF: 0.171 Hom.: 3139

Bravo AF: 0.130

Asia WGS AF: 0.219 AC: 762 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.2
DANN	Benign	0.40

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: rs1878007; hg19: chr3-172798800;