rs8134519

chr21-46182235-G-AchrNT_187626.1-43604-G-Achr21-46182235-G-TchrNT_187626.1-43604-G-Tchr21-46182235-G-CchrNT_187626.1-43604-G-C

Variant summary

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

The NM_001142854.2(SPATC1L):c.193+389C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.173 in 151,960 control chromosomes in the GnomAD database, including 2,748 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 0.17 (2748 hom., cov: 33)
• Consequence: SPATC1L NM_001142854.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.363

Genes affected

SPATC1L (HGNC:1298): (spermatogenesis and centriole associated 1 like) Enables identical protein binding activity. Predicted to act upstream of or within several processes, including actin polymerization or depolymerization; positive regulation of cAMP-dependent protein kinase activity; and positive regulation of protein kinase A signaling. Predicted to be located in sperm connecting piece. Predicted to be active in centrosome. [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=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.289 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SPATC1L	NM_001142854.2	c.193+389C>T		intron_variant		ENST00000291672.6
SPATC1L	NM_032261.5	c.-270+2121C>T		intron_variant
SPATC1L	XM_005261188.6	c.193+389C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SPATC1L	ENST00000291672.6	c.193+389C>T		intron_variant		2	NM_001142854.2	P1
SPATC1L	ENST00000330205.10	c.-270+2121C>T		intron_variant		1

Frequencies

GnomAD3 genomes AF: 0.173 AC: 26285 AN: 151840 Hom.: 2747 Cov.: 33

Gnomad AFR AF: 0.294

Gnomad AMI AF: 0.0804

Gnomad AMR AF: 0.116

Gnomad ASJ AF: 0.209

Gnomad EAS AF: 0.00116

Gnomad SAS AF: 0.0346

Gnomad FIN AF: 0.102

Gnomad MID AF: 0.187

Gnomad NFE AF: 0.146

Gnomad OTH AF: 0.174

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

GnomAD4 genome AF: 0.173 AC: 26303 AN: 151960 Hom.: 2748 Cov.: 33 AF XY: 0.166 AC XY: 12344 AN XY: 74330

Gnomad4 AFR AF: 0.294

Gnomad4 AMR AF: 0.116

Gnomad4 ASJ AF: 0.209

Gnomad4 EAS AF: 0.00117

Gnomad4 SAS AF: 0.0350

Gnomad4 FIN AF: 0.102

Gnomad4 NFE AF: 0.146

Gnomad4 OTH AF: 0.172

Alfa AF: 0.153 Hom.: 669

Bravo AF: 0.183

Asia WGS AF: 0.0400 AC: 140 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	0.15
Dann	Benign	0.79
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.2

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: rs8134519; hg19: chr21-47602149;