rs1515445

Variant names:

• chr3-173096605-G-A
• rs1515445
• NM_031955.6:c.612+20515C>T

Your query was ambiguous. Multiple possible variants found:

• chr3-173096605-G-A
• chr3-173096605-G-T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 4 publications found

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]

SPATA16 Gene-Disease associations (from GenCC):

• male infertility due to globozoospermia

  Inheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet
• spermatogenic failure 6

  Inheritance: AR Classification: LIMITED Submitted by: Labcorp Genetics (formerly Invitae)

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
SPATA16	NM_031955.6	c.612+20515C>T		intron_variant	Intron 2 of 10	ENST00000351008.4	NP_114161.3
SPATA16	XM_006713778.4	c.612+20515C>T		intron_variant	Intron 2 of 10		XP_006713841.1
SPATA16	XM_017007308.3	c.612+20515C>T		intron_variant	Intron 2 of 8		XP_016862797.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SPATA16	ENST00000351008.4	c.612+20515C>T		intron_variant	Intron 2 of 10	1	NM_031955.6	ENSP00000341765.3

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

African (AFR) AF: 0.165 AC: 6835 AN: 41476

American (AMR) AF: 0.0910 AC: 1390 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.137 AC: 475 AN: 3468

East Asian (EAS) AF: 0.0620 AC: 321 AN: 5178

South Asian (SAS) AF: 0.110 AC: 530 AN: 4820

European-Finnish (FIN) AF: 0.167 AC: 1764 AN: 10542

Middle Eastern (MID) AF: 0.102 AC: 30 AN: 294

European-Non Finnish (NFE) AF: 0.117 AC: 7919 AN: 67950

Other (OTH) AF: 0.115 AC: 241 AN: 2104

Alfa AF: 0.115 Hom.: 575

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
PhyloP100		-0.58
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs1515445; hg19: chr3-172814395;