rs1515445

chr3-173096605-G-Achr3-173096605-G-T

Variant summary

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

The NM_031955.6(SPATA16):c.612+20515C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.13 in 152,022 control chromosomes in the GnomAD database, including 1,342 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 0.13 (1342 hom., cov: 32)
• Consequence: SPATA16 NM_031955.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.580

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=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.162 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SPATA16	NM_031955.6	c.612+20515C>T		intron_variant		ENST00000351008.4
SPATA16	XM_006713778.4	c.612+20515C>T		intron_variant
SPATA16	XM_017007308.3	c.612+20515C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SPATA16	ENST00000351008.4	c.612+20515C>T		intron_variant		1	NM_031955.6	P1

Frequencies

GnomAD3 genomes AF: 0.130 AC: 19729 AN: 151904 Hom.: 1342 Cov.: 32

Gnomad AFR AF: 0.165

Gnomad AMI AF: 0.250

Gnomad AMR AF: 0.0911

Gnomad ASJ AF: 0.137

Gnomad EAS AF: 0.0620

Gnomad SAS AF: 0.110

Gnomad FIN AF: 0.167

Gnomad MID AF: 0.104

Gnomad NFE AF: 0.117

Gnomad OTH AF: 0.115

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

GnomAD4 genome AF: 0.130 AC: 19733 AN: 152022 Hom.: 1342 Cov.: 32 AF XY: 0.129 AC XY: 9577 AN XY: 74286

Gnomad4 AFR AF: 0.165

Gnomad4 AMR AF: 0.0910

Gnomad4 ASJ AF: 0.137

Gnomad4 EAS AF: 0.0620

Gnomad4 SAS AF: 0.110

Gnomad4 FIN AF: 0.167

Gnomad4 NFE AF: 0.117

Gnomad4 OTH AF: 0.115

Alfa AF: 0.115 Hom.: 514

Bravo AF: 0.126

Asia WGS AF: 0.0780 AC: 271 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	1.7
Dann	Benign	0.47

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: rs1515445; hg19: chr3-172814395;