rs1811763

chr3-173099816-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.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

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

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SPATA16	NM_031955.6	c.612+17304C>T		intron_variant		ENST00000351008.4
SPATA16	XM_006713778.4	c.612+17304C>T		intron_variant
SPATA16	XM_017007308.3	c.612+17304C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SPATA16	ENST00000351008.4	c.612+17304C>T		intron_variant		1	NM_031955.6	P1

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

Gnomad4 AFR AF: 0.0271

Gnomad4 AMR AF: 0.171

Gnomad4 ASJ AF: 0.0985

Gnomad4 EAS AF: 0.00154

Gnomad4 SAS AF: 0.120

Gnomad4 FIN AF: 0.120

Gnomad4 NFE AF: 0.143

Gnomad4 OTH AF: 0.0957

Alfa AF: 0.133 Hom.: 705

Bravo AF: 0.102

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	0.24
Dann	Benign	0.59

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: rs1811763; hg19: chr3-172817606;