2-200319165-G-A

Position:

• chr2-200319165-G-A

Variant summary

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

The NM_001100423.2(SPATS2L):​c.-72-10266G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.363 in 152,000 control chromosomes in the GnomAD database, including 11,365 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 0.36 (11365 hom., cov: 31)
• Consequence: SPATS2L NM_001100423.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.43

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=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.703 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SPATS2L	NM_001100423.2	c.-72-10266G>A		intron_variant		ENST00000409140.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SPATS2L	ENST00000409140.8	c.-72-10266G>A		intron_variant		2	NM_001100423.2	P1

Frequencies

GnomAD3 genomes AF: 0.363 AC: 55182 AN: 151882 Hom.: 11361 Cov.: 31

Gnomad AFR AF: 0.183

Gnomad AMI AF: 0.368

Gnomad AMR AF: 0.517

Gnomad ASJ AF: 0.379

Gnomad EAS AF: 0.723

Gnomad SAS AF: 0.505

Gnomad FIN AF: 0.450

Gnomad MID AF: 0.411

Gnomad NFE AF: 0.386

Gnomad OTH AF: 0.364

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

GnomAD4 genome AF: 0.363 AC: 55199 AN: 152000 Hom.: 11365 Cov.: 31 AF XY: 0.375 AC XY: 27868 AN XY: 74318

Gnomad4 AFR AF: 0.183

Gnomad4 AMR AF: 0.517

Gnomad4 ASJ AF: 0.379

Gnomad4 EAS AF: 0.723

Gnomad4 SAS AF: 0.505

Gnomad4 FIN AF: 0.450

Gnomad4 NFE AF: 0.386

Gnomad4 OTH AF: 0.365

Alfa AF: 0.305 Hom.: 1258

Bravo AF: 0.361

Asia WGS AF: 0.610 AC: 2115 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.0050
DANN	Benign	0.55

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: rs7605146; hg19: chr2-201183888;