2-200443394-T-C

Variant names:

• chr2-200443394-T-C
• rs1561296
• NM_001100423.2:c.788+2610T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001100423.2(SPATS2L):​c.788+2610T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.433 in 152,048 control chromosomes in the GnomAD database, including 16,024 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 0.43 (16024 hom., cov: 31)
• Consequence: SPATS2L NM_001100423.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.168
• Publications: 14 publications found

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]

ENSG00000287299 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.538 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001100423.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SPATS2L	NM_001100423.2	MANE Select	c.788+2610T>C		intron	N/A	NP_001093893.1
	SPATS2L	NM_001282744.2		c.878+2610T>C		intron	N/A	NP_001269673.1
	SPATS2L	NM_001100422.1		c.788+2610T>C		intron	N/A	NP_001093892.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SPATS2L	ENST00000409140.8	TSL:2 MANE Select	c.788+2610T>C		intron	N/A	ENSP00000386730.3
	SPATS2L	ENST00000358677.9	TSL:1	c.788+2610T>C		intron	N/A	ENSP00000351503.4
	SPATS2L	ENST00000360760.9	TSL:1	c.581+2610T>C		intron	N/A	ENSP00000353989.5

Frequencies

GnomAD3 genomes AF: 0.434 AC: 65870 AN: 151930 Hom.: 16020 Cov.: 31

Gnomad AFR AF: 0.211

Gnomad AMI AF: 0.506

Gnomad AMR AF: 0.513

Gnomad ASJ AF: 0.439

Gnomad EAS AF: 0.231

Gnomad SAS AF: 0.448

Gnomad FIN AF: 0.568

Gnomad MID AF: 0.402

Gnomad NFE AF: 0.543

Gnomad OTH AF: 0.461

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

GnomAD4 genome AF: 0.433 AC: 65880 AN: 152048 Hom.: 16024 Cov.: 31 AF XY: 0.435 AC XY: 32319 AN XY: 74340

African (AFR) AF: 0.210 AC: 8722 AN: 41478

American (AMR) AF: 0.513 AC: 7835 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.439 AC: 1524 AN: 3470

East Asian (EAS) AF: 0.232 AC: 1198 AN: 5174

South Asian (SAS) AF: 0.448 AC: 2161 AN: 4822

European-Finnish (FIN) AF: 0.568 AC: 6000 AN: 10564

Middle Eastern (MID) AF: 0.398 AC: 117 AN: 294

European-Non Finnish (NFE) AF: 0.543 AC: 36900 AN: 67958

Other (OTH) AF: 0.457 AC: 965 AN: 2112

Alfa AF: 0.511 Hom.: 32835

Bravo AF: 0.423

Asia WGS AF: 0.312 AC: 1088 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	2.4
DANN	Benign	0.52
PhyloP100		-0.17
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs1561296; hg19: chr2-201308117;