9-4594919-C-G

Position:

• chr9-4594919-C-G

Variant summary

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

The ENST00000461761.5(SPATA6L):​c.*254+1516G>C variant causes a intron, NMD transcript 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, NMD_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.14

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

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SPATA6L	NR_148444.2	n.1754+5734G>C		intron_variant, non_coding_transcript_variant
SPATA6L	NR_148445.2	n.1663+1516G>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SPATA6L	ENST00000461761.5	c.*254+1516G>C		intron_variant, NMD_transcript_variant		2		ENSP00000418458
SPATA6L	ENST00000485616.5	c.*781+5734G>C		intron_variant, NMD_transcript_variant		2		ENSP00000420003
SPATA6L	ENST00000486047.5	c.*1106+5734G>C		intron_variant, NMD_transcript_variant		2		ENSP00000417965

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

Gnomad4 AFR AF: 0.830

Gnomad4 AMR AF: 0.590

Gnomad4 ASJ AF: 0.671

Gnomad4 EAS AF: 0.467

Gnomad4 SAS AF: 0.693

Gnomad4 FIN AF: 0.660

Gnomad4 NFE AF: 0.699

Gnomad4 OTH AF: 0.706

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 v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs301443; hg19: chr9-4594919;