Variant chr2-200439125-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2

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. 14/20 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

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: 2.82

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]

SPATS2L links:

(HGNC:):

links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -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/exons	MANE	UniProt
SPATS2L	NM_001100423.2 linkuse as main transcript	c.449G>A	p.Gly150Asp	missense_variant	7/13	ENST00000409140.8
LOC101927741	XR_007088047.1 linkuse as main transcript	n.663-7588C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SPATS2L	ENST00000409140.8 linkuse as main transcript	c.449G>A	p.Gly150Asp	missense_variant	7/13	2	NM_001100423.2	P1	Q9NUQ6-1
	ENST00000655656.1 linkuse as main transcript	n.567-7588C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes

AF:

0.00248

AC:

377

AN:

152144

Hom.:

Cov.:

show subpopulations

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

GnomAD3 exomes

AF:

0.00264

AC:

655

AN:

248574

Hom.:

AF XY:

0.00269

AC XY:

363

AN XY:

134824

show subpopulations

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 SAS exome

AF:

0.00124

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.:

Cov.:

AF XY:

0.00413

AC XY:

2997

AN XY:

726510

show subpopulations

Gnomad4 AFR exome

AF:

0.000628

Gnomad4 AMR exome

AF:

0.00143

Gnomad4 ASJ exome

AF:

0.0000383

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.00121

Gnomad4 FIN exome

AF:

0.00242

Gnomad4 NFE exome

AF:

0.00514

Gnomad4 OTH exome

AF:

0.00327

GnomAD4 genome

AF:

0.00248

AC:

377

AN:

152262

Hom.:

Cov.:

AF XY:

0.00223

AC XY:

166

AN XY:

74452

show subpopulations

Gnomad4 AFR

AF:

0.000891

Gnomad4 AMR

AF:

0.00222

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.000415

Gnomad4 FIN

AF:

0.00179

Gnomad4 NFE

AF:

0.00409

Gnomad4 OTH

AF:

0.00284

Alfa

AF:

0.00381

Hom.:

Bravo

AF:

0.00225

TwinsUK

AF:

0.00539

AC:

ALSPAC

AF:

0.00493

AC:

ESP6500AA

AF:

0.000797

AC:

ESP6500EA

AF:

0.00425

AC:

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

LINK: link

Submissions by phenotype

not provided

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

Invitae

Jun 21, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.093

BayesDel_addAF

Benign

-0.31

BayesDel_noAF

Benign

-0.22

CADD

Benign

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

LIST_S2

Benign

0.85

.;.;.;T;.;T;T;T;T;T

M_CAP

Benign

0.0054

MetaRNN

Benign

0.0069

T;T;T;T;T;T;T;T;T;T

MetaSVM

Benign

-0.87

MutationAssessor

Benign

1.6

L;L;L;.;L;.;L;.;.;.

MutationTaster

Benign

1.0

D;D;D;D;D;D;D;D;D

PrimateAI

Benign

0.45

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

GERP RS

5.2

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

Varity_R

0.14

gMVP

0.55

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

Publications

LitVar

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

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over