rs12553697

Variant names:

• chr9-4591655-T-C
• rs12553697
• ENST00000461761.5:n.*255-2694A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000461761.5(SPATA6L):​n.*255-2694A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.104 in 152,248 control chromosomes in the GnomAD database, including 932 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 (932 hom., cov: 32)
• Consequence: SPATA6L ENST00000461761.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.137
• Publications: 4 publications found

Genes affected

SPATA6L (HGNC:25472): (spermatogenesis associated 6 like) Predicted to enable myosin light chain binding activity. Predicted to be involved in spermatogenesis. Predicted to be located in sperm connecting piece. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.7).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.121 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000461761.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SPATA6L	NR_148444.2		n.1755-2694A>G		intron	N/A
	SPATA6L	NR_148445.2		n.1664-2694A>G		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SPATA6L	ENST00000461761.5	TSL:2	n.*255-2694A>G		intron	N/A	ENSP00000418458.1	Q8N4H0-1
	SPATA6L	ENST00000485616.5	TSL:2	n.*781+8998A>G		intron	N/A	ENSP00000420003.1	D3DRI0
	SPATA6L	ENST00000486047.5	TSL:2	n.*1107-2694A>G		intron	N/A	ENSP00000417965.1	Q8N4H0-2

Frequencies

GnomAD3 genomes AF: 0.104 AC: 15856 AN: 152130 Hom.: 934 Cov.: 32

Gnomad AFR AF: 0.0715

Gnomad AMI AF: 0.101

Gnomad AMR AF: 0.0728

Gnomad ASJ AF: 0.153

Gnomad EAS AF: 0.130

Gnomad SAS AF: 0.128

Gnomad FIN AF: 0.162

Gnomad MID AF: 0.231

Gnomad NFE AF: 0.115

Gnomad OTH AF: 0.115

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

GnomAD4 genome AF: 0.104 AC: 15856 AN: 152248 Hom.: 932 Cov.: 32 AF XY: 0.107 AC XY: 7971 AN XY: 74436

African (AFR) AF: 0.0714 AC: 2968 AN: 41544

American (AMR) AF: 0.0727 AC: 1113 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.153 AC: 530 AN: 3470

East Asian (EAS) AF: 0.130 AC: 671 AN: 5180

South Asian (SAS) AF: 0.128 AC: 618 AN: 4822

European-Finnish (FIN) AF: 0.162 AC: 1717 AN: 10598

Middle Eastern (MID) AF: 0.231 AC: 68 AN: 294

European-Non Finnish (NFE) AF: 0.115 AC: 7838 AN: 68016

Other (OTH) AF: 0.114 AC: 241 AN: 2114

Alfa AF: 0.109 Hom.: 1775

Bravo AF: 0.0947

Asia WGS AF: 0.109 AC: 377 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.70
CADD	Benign	3.3
DANN	Benign	0.91
PhyloP100		0.14

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs12553697;

hg19: chr9-4591655;