X-21978023-C-T

Position:

chrX-21978023-C-T

Variant summary

Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP4_StrongBP6_Very_StrongBS2

The NM_004595.5(SMS):c.569C>T(p.Thr190Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000132 in 1,206,163 control chromosomes in the GnomAD database, including 1 homozygotes. There are 53 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).

Frequency

Genomes: 𝑓 0.000090 ( 0 hom., 6 hem., cov: 23)

Exomes 𝑓: 0.00014 ( 1 hom. 47 hem. )

Consequence

SMS
NM_004595.5 missense

Scores

Clinical Significance

Benign/Likely benign criteria provided, multiple submitters, no conflicts B:3

Conservation

PhyloP100: 3.08

Variant links:

Genes affected

SMS (HGNC:11123): (spermine synthase) This gene encodes a protein belonging to the spermidine/spermin synthase family and catalyzes the production of spermine from spermidine. Pseudogenes of this gene are located on chromosomes 1, 5, 6 and X. Mutations in this gene cause an X-linked intellectual disability called Snyder-Robinson Syndrome (SRS). Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2017]

SMS links:

SMS (HGNC:):

SMS links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -16 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.024828196).

BP6

Variant X-21978023-C-T is Benign according to our data. Variant chrX-21978023-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 198177.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chrX-21978023-C-T is described in Lovd as [Likely_benign].

BS2

High Hemizygotes in GnomAd4 at 6 XL gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SMS	NM_004595.5 linkuse as main transcript	c.569C>T	p.Thr190Ile	missense_variant	6/11	ENST00000404933.7	NP_004586.2	P52788-1
SMS	NM_001258423.2 linkuse as main transcript	c.410C>T	p.Thr137Ile	missense_variant	4/9		NP_001245352.1	P52788-2
SMS	XM_005274582.3 linkuse as main transcript	c.467C>T	p.Thr156Ile	missense_variant	6/11		XP_005274639.1
SMS	XM_011545568.3 linkuse as main transcript	c.467C>T	p.Thr156Ile	missense_variant	6/11		XP_011543870.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	UniProt
SMS	ENST00000404933.7 linkuse as main transcript	c.569C>T	p.Thr190Ile	missense_variant	6/11	1	NM_004595.5	ENSP00000385746.2	P52788-1
SMS	ENST00000457085.2 linkuse as main transcript	c.914C>T	p.Thr305Ile	missense_variant	6/6	5		ENSP00000407366.2	H7C2R7
SMS	ENST00000379404.5 linkuse as main transcript	c.410C>T	p.Thr137Ile	missense_variant	4/9	3		ENSP00000368714.1	P52788-2
SMS	ENST00000478094.1 linkuse as main transcript	n.*34C>T		downstream_gene_variant		4

Frequencies

GnomAD3 genomes

AF:

0.0000896

AC:

AN:

111610

Hom.:

Cov.:

AF XY:

0.000178

AC XY:

AN XY:

33768

show subpopulations

Gnomad AFR

AF:

0.00

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00280

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00

Gnomad OTH

AF:

0.00

GnomAD3 exomes

AF:

0.000185

AC:

AN:

183493

Hom.:

AF XY:

0.000147

AC XY:

AN XY:

67929

show subpopulations

Gnomad AFR exome

AF:

0.00

Gnomad AMR exome

AF:

0.00

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.00238

Gnomad SAS exome

AF:

0.00

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.0000122

Gnomad OTH exome

AF:

0.00

GnomAD4 exome

AF:

0.000136

AC:

149

AN:

1094497

Hom.:

Cov.:

AF XY:

0.000131

AC XY:

AN XY:

359929

show subpopulations

Gnomad4 AFR exome

AF:

0.00

Gnomad4 AMR exome

AF:

0.00

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.00480

Gnomad4 SAS exome

AF:

0.0000185

Gnomad4 FIN exome

AF:

0.00

Gnomad4 NFE exome

AF:

0.00000238

Gnomad4 OTH exome

AF:

0.0000218

GnomAD4 genome

AF:

0.0000896

AC:

AN:

111666

Hom.:

Cov.:

AF XY:

0.000177

AC XY:

AN XY:

33834

show subpopulations

Gnomad4 AFR

AF:

0.00

Gnomad4 AMR

AF:

0.00

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.00281

Gnomad4 SAS

AF:

0.00

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.00

Gnomad4 OTH

AF:

0.00

Alfa

AF:

0.0000712

Hom.:

Bravo

AF:

0.000106

ExAC

AF:

0.000206

AC:

ClinVar

Significance: Benign/Likely benign

Submissions summary: Benign:3

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not specified

Benign:1

Benign, criteria provided, single submitter

clinical testing

Eurofins Ntd Llc (ga)

Mar 06, 2015

- -

Inborn genetic diseases

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

Ambry Genetics

Aug 19, 2016

This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. -

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

Labcorp Genetics (formerly Invitae), Labcorp

Dec 31, 2019

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.12

BayesDel_addAF

Benign

-0.39

BayesDel_noAF

Benign

-0.33

CADD

Benign

DANN

Uncertain

1.0

DEOGEN2

Benign

0.16

T;.

FATHMM_MKL

Uncertain

0.94

LIST_S2

Benign

0.72

T;T

M_CAP

Pathogenic

0.60

MetaRNN

Benign

0.025

T;T

MetaSVM

Benign

-0.42

MutationAssessor

Uncertain

2.3

M;.

PrimateAI

Uncertain

0.56

PROVEAN

Uncertain

-3.0

D;D

REVEL

Benign

0.27

Sift

Benign

0.049

D;T

Sift4G

Benign

0.14

T;T

Polyphen

0.099

B;P

Vest4

0.30

MVP

0.74

MPC

1.1

ClinPred

0.13

GERP RS

3.8

Varity_R

0.39

gMVP

0.67

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.

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