rs11720607

Positions:

• chr3-173125487-T-G

Variant summary

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

The ENST00000351008.4(SPATA16):​c.-18-7738A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.225 in 152,100 control chromosomes in the GnomAD database, including 4,629 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 0.22 (4629 hom., cov: 32)
• Consequence: SPATA16 ENST00000351008.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.05

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]

LOC105374220 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.375 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SPATA16	NM_031955.6	c.-18-7738A>C		intron_variant		ENST00000351008.4	NP_114161.3
LOC105374220	XR_001741021.1	n.65+11135T>G		intron_variant, non_coding_transcript_variant
SPATA16	XM_006713778.4	c.-18-7738A>C		intron_variant			XP_006713841.1
SPATA16	XM_017007308.3	c.-18-7738A>C		intron_variant			XP_016862797.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SPATA16	ENST00000351008.4	c.-18-7738A>C		intron_variant		1	NM_031955.6	ENSP00000341765	P1

Frequencies

GnomAD3 genomes AF: 0.225 AC: 34174 AN: 151982 Hom.: 4612 Cov.: 32

Gnomad AFR AF: 0.380

Gnomad AMI AF: 0.288

Gnomad AMR AF: 0.145

Gnomad ASJ AF: 0.194

Gnomad EAS AF: 0.0648

Gnomad SAS AF: 0.169

Gnomad FIN AF: 0.209

Gnomad MID AF: 0.187

Gnomad NFE AF: 0.169

Gnomad OTH AF: 0.206

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

GnomAD4 genome AF: 0.225 AC: 34211 AN: 152100 Hom.: 4629 Cov.: 32 AF XY: 0.222 AC XY: 16530 AN XY: 74360

Gnomad4 AFR AF: 0.380

Gnomad4 AMR AF: 0.145

Gnomad4 ASJ AF: 0.194

Gnomad4 EAS AF: 0.0648

Gnomad4 SAS AF: 0.168

Gnomad4 FIN AF: 0.209

Gnomad4 NFE AF: 0.169

Gnomad4 OTH AF: 0.203

Alfa AF: 0.173 Hom.: 2523

Bravo AF: 0.228

Asia WGS AF: 0.128 AC: 448 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.20
DANN	Benign	0.73

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: rs11720607; hg19: chr3-172843277; COSMIC: COSV63526120;