2-200419253-A-G

Variant summary

Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4

The NM_001100423.2(SPATS2L):ā€‹c.202A>Gā€‹(p.Asn68Asp) variant causes a missense change. The variant allele was found at a frequency of 0.000021 in 1,567,918 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā˜…).

Frequency

Genomes: š‘“ 0.000026 ( 0 hom., cov: 32)
Exomes š‘“: 0.000020 ( 0 hom. )

Consequence

SPATS2L
NM_001100423.2 missense

Scores

1
6
12

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 4.21
Variant links:
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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 1 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.31477284).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
SPATS2LNM_001100423.2 linkuse as main transcriptc.202A>G p.Asn68Asp missense_variant 6/13 ENST00000409140.8 NP_001093893.1
LOC101927741XR_007088047.1 linkuse as main transcriptn.911-7745T>C intron_variant, non_coding_transcript_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
SPATS2LENST00000409140.8 linkuse as main transcriptc.202A>G p.Asn68Asp missense_variant 6/132 NM_001100423.2 ENSP00000386730 P1Q9NUQ6-1
ENST00000655656.1 linkuse as main transcriptn.814+10170T>C intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes
AF:
0.0000263
AC:
4
AN:
152170
Hom.:
0
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0000241
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.0000441
Gnomad OTH
AF:
0.00
GnomAD4 exome
AF:
0.0000205
AC:
29
AN:
1415748
Hom.:
0
Cov.:
31
AF XY:
0.0000229
AC XY:
16
AN XY:
699838
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.0000267
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
AF:
0.0000263
AC:
4
AN:
152170
Hom.:
0
Cov.:
32
AF XY:
0.0000404
AC XY:
3
AN XY:
74340
show subpopulations
Gnomad4 AFR
AF:
0.0000241
Gnomad4 AMR
AF:
0.00
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.0000441
Gnomad4 OTH
AF:
0.00
Alfa
AF:
0.000142
Hom.:
0
Bravo
AF:
0.0000302

ClinVar

Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not specified Uncertain:1
Uncertain significance, criteria provided, single submitterclinical testingAmbry GeneticsMar 18, 2024The c.202A>G (p.N68D) alteration is located in exon 6 (coding exon 4) of the SPATS2L gene. This alteration results from a A to G substitution at nucleotide position 202, causing the asparagine (N) at amino acid position 68 to be replaced by an aspartic acid (D). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Pathogenic
0.88
BayesDel_addAF
Benign
-0.044
T
BayesDel_noAF
Benign
-0.30
CADD
Pathogenic
26
DANN
Uncertain
1.0
DEOGEN2
Benign
0.039
T;T;T;T;T;T;T;.;T;T;T;T;T;.;.;.;.;.
Eigen
Uncertain
0.55
Eigen_PC
Uncertain
0.58
FATHMM_MKL
Uncertain
0.95
D
LIST_S2
Uncertain
0.93
D;.;.;.;D;D;.;D;D;D;D;D;D;D;D;D;D;D
M_CAP
Benign
0.0063
T
MetaRNN
Benign
0.31
T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T
MetaSVM
Benign
-0.50
T
MutationAssessor
Benign
1.8
.;L;L;L;.;.;L;L;.;.;.;L;.;.;.;.;.;.
MutationTaster
Benign
0.98
D;D;D;D;D;D;D;D;D
PrimateAI
Uncertain
0.73
T
PROVEAN
Benign
-2.2
N;N;N;N;N;N;N;N;N;N;N;N;N;.;N;N;N;N
REVEL
Benign
0.12
Sift
Benign
0.096
T;T;T;T;D;T;T;T;T;T;D;T;T;.;T;T;T;T
Sift4G
Benign
0.17
T;T;T;T;T;T;T;T;T;T;T;T;T;T;.;T;T;T
Polyphen
0.99, 0.93
.;D;D;D;.;.;D;P;.;.;.;D;.;.;.;.;.;.
Vest4
0.43, 0.36, 0.41, 0.42
MutPred
0.34
Gain of helix (P = 0.0854);Gain of helix (P = 0.0854);Gain of helix (P = 0.0854);Gain of helix (P = 0.0854);.;Gain of helix (P = 0.0854);Gain of helix (P = 0.0854);Gain of helix (P = 0.0854);Gain of helix (P = 0.0854);Gain of helix (P = 0.0854);Gain of helix (P = 0.0854);Gain of helix (P = 0.0854);Gain of helix (P = 0.0854);.;.;Gain of helix (P = 0.0854);Gain of helix (P = 0.0854);.;
MVP
0.23
MPC
1.0
ClinPred
0.87
D
GERP RS
5.6
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.7
Varity_R
0.23
gMVP
0.35

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

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs1261003667; hg19: chr2-201283976; API