rs192861441

Variant names:

• chr2-200439125-G-A
• rs192861441
• NM_001100423.2:c.449G>A

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Strong BP6_Moderate BS2

The NM_001100423.2(SPATS2L):​c.449G>A​(p.Gly150Asp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00409 in 1,612,540 control chromosomes in the GnomAD database, including 14 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

• Frequency:
  • Genomes: 𝑓 0.0025 (0 hom., cov: 32)
  • Exomes 𝑓: 0.0043 (14 hom.)
• Consequence: SPATS2L NM_001100423.2 missense
• Clinical Significance: Likely benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 2.82
• Publications: 2 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 -10 ACMG points.

• BP4: Computational evidence support a benign effect (MetaRNN=0.006936401).
• BP6: Variant 2-200439125-G-A is Benign according to our data. Variant chr2-200439125-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 718410.Status of the report is criteria_provided_single_submitter, 1 stars.
• BS2: High Homozygotes in GnomAdExome4 at 14 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SPATS2L	NM_001100423.2	c.449G>A	p.Gly150Asp	missense_variant	Exon 7 of 13	ENST00000409140.8	NP_001093893.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SPATS2L	ENST00000409140.8	c.449G>A	p.Gly150Asp	missense_variant	Exon 7 of 13	2	NM_001100423.2	ENSP00000386730.3

Frequencies

GnomAD3 genomes AF: 0.00248 AC: 377 AN: 152144 Hom.: 0 Cov.: 32

Gnomad AFR AF: 0.000893

Gnomad AMI AF: 0.00110

Gnomad AMR AF: 0.00223

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.000414

Gnomad FIN AF: 0.00179

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00409

Gnomad OTH AF: 0.00287

GnomAD2 exomes AF: 0.00264 AC: 655 AN: 248574 AF XY: 0.00269

Gnomad AFR exome AF: 0.00103

Gnomad AMR exome AF: 0.00122

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.00

Gnomad FIN exome AF: 0.00237

Gnomad NFE exome AF: 0.00426

Gnomad OTH exome AF: 0.00465

GnomAD4 exome AF: 0.00426 AC: 6226 AN: 1460278 Hom.: 14 Cov.: 31 AF XY: 0.00413 AC XY: 2997 AN XY: 726510

African (AFR) AF: 0.000628 AC: 21 AN: 33430

American (AMR) AF: 0.00143 AC: 64 AN: 44664

Ashkenazi Jewish (ASJ) AF: 0.0000383 AC: 1 AN: 26112

East Asian (EAS) AF: 0.00 AC: 0 AN: 39668

South Asian (SAS) AF: 0.00121 AC: 104 AN: 86222

European-Finnish (FIN) AF: 0.00242 AC: 129 AN: 53394

Middle Eastern (MID) AF: 0.000869 AC: 5 AN: 5752

European-Non Finnish (NFE) AF: 0.00514 AC: 5705 AN: 1110720

Other (OTH) AF: 0.00327 AC: 197 AN: 60316

GnomAD4 genome AF: 0.00248 AC: 377 AN: 152262 Hom.: 0 Cov.: 32 AF XY: 0.00223 AC XY: 166 AN XY: 74452

African (AFR) AF: 0.000891 AC: 37 AN: 41546

American (AMR) AF: 0.00222 AC: 34 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3470

East Asian (EAS) AF: 0.00 AC: 0 AN: 5186

South Asian (SAS) AF: 0.000415 AC: 2 AN: 4824

European-Finnish (FIN) AF: 0.00179 AC: 19 AN: 10612

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 294

European-Non Finnish (NFE) AF: 0.00409 AC: 278 AN: 68022

Other (OTH) AF: 0.00284 AC: 6 AN: 2116

Alfa AF: 0.00358 Hom.: 2

Bravo AF: 0.00225

TwinsUK AF: 0.00539 AC: 20

ALSPAC AF: 0.00493 AC: 19

ESP6500AA AF: 0.000797 AC: 3

ESP6500EA AF: 0.00425 AC: 35

ExAC AF: 0.00271 AC: 328

EpiCase AF: 0.00458

EpiControl AF: 0.00368

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Jun 21, 2018

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Likely benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.093
BayesDel_addAF	Benign	-0.31	T
BayesDel_noAF	Benign	-0.22
CADD	Benign	22
DANN	Uncertain	0.98
DEOGEN2	Benign	0.0017	T;T;T;T;T;T;T;.;.;.
Eigen	Benign	0.13
Eigen_PC	Uncertain	0.26
FATHMM_MKL	Uncertain	0.93	D
LIST_S2	Benign	0.85	.;.;.;T;.;T;T;T;T;T
M_CAP	Benign	0.0054	T
MetaRNN	Benign	0.0069	T;T;T;T;T;T;T;T;T;T
MetaSVM	Benign	-0.87	T
MutationAssessor	Benign	1.6	L;L;L;.;L;.;L;.;.;.
PhyloP100		2.8
PrimateAI	Benign	0.45	T
PROVEAN	Benign	-0.79	N;N;N;N;N;N;N;.;N;N
REVEL	Benign	0.10
Sift	Benign	0.38	T;T;T;T;T;T;T;.;T;D
Sift4G	Benign	0.63	T;T;T;T;T;T;T;T;.;T
Polyphen		0.51	P;P;P;.;P;.;P;.;.;.
Vest4		0.21
MVP		0.043
MPC		0.70
ClinPred		0.015	T
GERP RS		5.2
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1
Varity_R		0.14
gMVP		0.55
Mutation Taster		=71/29	polymorphism

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.12		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: rs192861441; hg19: chr2-201303848;