rs1811763

Variant names:

• chr3-173099816-G-A
• rs1811763
• NM_031955.6:c.612+17304C>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+17304C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.105 in 152,178 control chromosomes in the GnomAD database, including 1,104 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 0.10 (1104 hom., cov: 32)
• Consequence: SPATA16 NM_031955.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.17
• Publications: 6 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)

ENSG00000237473 (HGNC:):

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 (AMR) allele frequency at 95% confidence interval = 0.165 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_031955.6. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SPATA16	NM_031955.6	MANE Select	c.612+17304C>T		intron	N/A	NP_114161.3

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SPATA16	ENST00000351008.4	TSL:1 MANE Select	c.612+17304C>T		intron	N/A	ENSP00000341765.3
	ENSG00000237473	ENST00000824748.1		n.175+414G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.105 AC: 15951 AN: 152060 Hom.: 1106 Cov.: 32

Gnomad AFR AF: 0.0272

Gnomad AMI AF: 0.0581

Gnomad AMR AF: 0.171

Gnomad ASJ AF: 0.0985

Gnomad EAS AF: 0.00154

Gnomad SAS AF: 0.120

Gnomad FIN AF: 0.120

Gnomad MID AF: 0.0791

Gnomad NFE AF: 0.143

Gnomad OTH AF: 0.0967

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

GnomAD4 genome AF: 0.105 AC: 15945 AN: 152178 Hom.: 1104 Cov.: 32 AF XY: 0.105 AC XY: 7782 AN XY: 74380

African (AFR) AF: 0.0271 AC: 1124 AN: 41526

American (AMR) AF: 0.171 AC: 2608 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.0985 AC: 342 AN: 3472

East Asian (EAS) AF: 0.00154 AC: 8 AN: 5180

South Asian (SAS) AF: 0.120 AC: 577 AN: 4822

European-Finnish (FIN) AF: 0.120 AC: 1274 AN: 10592

Middle Eastern (MID) AF: 0.0748 AC: 22 AN: 294

European-Non Finnish (NFE) AF: 0.143 AC: 9735 AN: 67998

Other (OTH) AF: 0.0957 AC: 202 AN: 2110

Alfa AF: 0.127 Hom.: 941

Bravo AF: 0.102

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.24
DANN	Benign	0.59
PhyloP100		-1.2
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: rs1811763; hg19: chr3-172817606;