rs3754793

Positions:

• chr2-200443670-A-C
• chr2-200443670-A-T

Variant summary

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

The NM_001100423.2(SPATS2L):​c.788+2886A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.316 in 152,054 control chromosomes in the GnomAD database, including 7,924 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 0.32 (7924 hom., cov: 31)
• Consequence: SPATS2L NM_001100423.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.178

Genes affected

SPATS2L (HGNC:24574): (spermatogenesis associated serine rich 2 like) Enables RNA binding activity. Located in cytosol; nucleolus; and nucleoplasm. Part of protein-containing complex. [provided by Alliance of Genome Resources, Apr 2022]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.406 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SPATS2L	NM_001100423.2	c.788+2886A>C		intron_variant		ENST00000409140.8
LOC101927741	XR_007088047.1	n.662+5706T>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SPATS2L	ENST00000409140.8	c.788+2886A>C		intron_variant		2	NM_001100423.2	P1
	ENST00000655656.1	n.567-12133T>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.316 AC: 48061 AN: 151938 Hom.: 7919 Cov.: 31

Gnomad AFR AF: 0.213

Gnomad AMI AF: 0.349

Gnomad AMR AF: 0.303

Gnomad ASJ AF: 0.385

Gnomad EAS AF: 0.415

Gnomad SAS AF: 0.421

Gnomad FIN AF: 0.313

Gnomad MID AF: 0.415

Gnomad NFE AF: 0.363

Gnomad OTH AF: 0.328

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

GnomAD4 genome AF: 0.316 AC: 48077 AN: 152054 Hom.: 7924 Cov.: 31 AF XY: 0.316 AC XY: 23480 AN XY: 74320

Gnomad4 AFR AF: 0.213

Gnomad4 AMR AF: 0.303

Gnomad4 ASJ AF: 0.385

Gnomad4 EAS AF: 0.415

Gnomad4 SAS AF: 0.421

Gnomad4 FIN AF: 0.313

Gnomad4 NFE AF: 0.363

Gnomad4 OTH AF: 0.333

Alfa AF: 0.335 Hom.: 1382

Bravo AF: 0.311

Asia WGS AF: 0.439 AC: 1525 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	2.0
DANN	Benign	0.64

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: rs3754793; hg19: chr2-201308393;