2-200389448-A-G

Position:

• chr2-200389448-A-G

Variant summary

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

The NM_001100423.2(SPATS2L):​c.39+165A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.683 in 533,408 control chromosomes in the GnomAD database, including 126,559 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 0.65 (32773 hom., cov: 33)
  • Exomes 𝑓: 0.70 (93786 hom.)
• Consequence: SPATS2L NM_001100423.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.480

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]

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 (SAS) allele frequency at 95% confidence interval = 0.789 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SPATS2L	NM_001100423.2	c.39+165A>G		intron_variant		ENST00000409140.8	NP_001093893.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SPATS2L	ENST00000409140.8	c.39+165A>G		intron_variant		2	NM_001100423.2	ENSP00000386730	P1

Frequencies

GnomAD3 genomes AF: 0.645 AC: 98121 AN: 152036 Hom.: 32747 Cov.: 33

Gnomad AFR AF: 0.463

Gnomad AMI AF: 0.653

Gnomad AMR AF: 0.741

Gnomad ASJ AF: 0.733

Gnomad EAS AF: 0.675

Gnomad SAS AF: 0.811

Gnomad FIN AF: 0.722

Gnomad MID AF: 0.682

Gnomad NFE AF: 0.704

Gnomad OTH AF: 0.650

GnomAD4 exome AF: 0.698 AC: 266265 AN: 381254 Hom.: 93786 Cov.: 4 AF XY: 0.703 AC XY: 140637 AN XY: 200036

Gnomad4 AFR exome AF: 0.477

Gnomad4 AMR exome AF: 0.761

Gnomad4 ASJ exome AF: 0.736

Gnomad4 EAS exome AF: 0.660

Gnomad4 SAS exome AF: 0.794

Gnomad4 FIN exome AF: 0.696

Gnomad4 NFE exome AF: 0.697

Gnomad4 OTH exome AF: 0.685

GnomAD4 genome AF: 0.645 AC: 98200 AN: 152154 Hom.: 32773 Cov.: 33 AF XY: 0.656 AC XY: 48774 AN XY: 74382

Gnomad4 AFR AF: 0.464

Gnomad4 AMR AF: 0.741

Gnomad4 ASJ AF: 0.733

Gnomad4 EAS AF: 0.675

Gnomad4 SAS AF: 0.811

Gnomad4 FIN AF: 0.722

Gnomad4 NFE AF: 0.704

Gnomad4 OTH AF: 0.650

Alfa AF: 0.692 Hom.: 35642

Bravo AF: 0.636

Asia WGS AF: 0.720 AC: 2505 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	0.14
DANN	Benign	0.38

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: rs4674015; hg19: chr2-201254171; COSMIC: COSV62353686; COSMIC: COSV62353686;