9-4594919-C-G

Variant names:

• chr9-4594919-C-G
• rs301443
• ENST00000461761.5:n.*254+1516G>C

Variant summary

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

The ENST00000461761.5(SPATA6L):​n.*254+1516G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.713 in 152,012 control chromosomes in the GnomAD database, including 39,318 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 0.71 (39318 hom., cov: 31)
• Consequence: SPATA6L ENST00000461761.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.14
• Publications: 18 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=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.823 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.1754+5734G>C		intron	N/A
	SPATA6L	NR_148445.2		n.1663+1516G>C		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SPATA6L	ENST00000461761.5	TSL:2	n.*254+1516G>C		intron	N/A	ENSP00000418458.1	Q8N4H0-1
	SPATA6L	ENST00000485616.5	TSL:2	n.*781+5734G>C		intron	N/A	ENSP00000420003.1	D3DRI0
	SPATA6L	ENST00000486047.5	TSL:2	n.*1106+5734G>C		intron	N/A	ENSP00000417965.1	Q8N4H0-2

Frequencies

GnomAD3 genomes AF: 0.713 AC: 108288 AN: 151894 Hom.: 39280 Cov.: 31

Gnomad AFR AF: 0.830

Gnomad AMI AF: 0.726

Gnomad AMR AF: 0.591

Gnomad ASJ AF: 0.671

Gnomad EAS AF: 0.467

Gnomad SAS AF: 0.694

Gnomad FIN AF: 0.660

Gnomad MID AF: 0.778

Gnomad NFE AF: 0.699

Gnomad OTH AF: 0.702

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

GnomAD4 genome AF: 0.713 AC: 108385 AN: 152012 Hom.: 39318 Cov.: 31 AF XY: 0.707 AC XY: 52569 AN XY: 74304

African (AFR) AF: 0.830 AC: 34423 AN: 41462

American (AMR) AF: 0.590 AC: 9021 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.671 AC: 2325 AN: 3466

East Asian (EAS) AF: 0.467 AC: 2416 AN: 5168

South Asian (SAS) AF: 0.693 AC: 3336 AN: 4814

European-Finnish (FIN) AF: 0.660 AC: 6958 AN: 10542

Middle Eastern (MID) AF: 0.782 AC: 230 AN: 294

European-Non Finnish (NFE) AF: 0.699 AC: 47530 AN: 67972

Other (OTH) AF: 0.706 AC: 1485 AN: 2104

Alfa AF: 0.701 Hom.: 4676

Bravo AF: 0.710

Asia WGS AF: 0.625 AC: 2178 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.050
DANN	Benign	0.74
PhyloP100		-1.1

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: rs301443;

hg19: chr9-4594919;