rs769360962

Variant names:

Your query was ambiguous. Multiple possible variants found:

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBP6_Very_Strong

The NM_015001.3(SPEN):c.9736A>C(p.Thr3246Pro) variant causes a missense change involving the alteration of a non-conserved nucleotide. 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 Benign (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. T3246I) has been classified as Uncertain significance.

Frequency

Genomes: 𝑓 0.24 ( 0 hom., cov: 0)

Exomes 𝑓: 0.068 ( 0 hom. )

Failed GnomAD Quality Control

Consequence

SPEN
NM_015001.3 missense

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:3

Conservation

PhyloP100: -0.543

Variant links:

Genes affected

SPEN (HGNC:17575): (spen family transcriptional repressor) This gene encodes a hormone inducible transcriptional repressor. Repression of transcription by this gene product can occur through interactions with other repressors, by the recruitment of proteins involved in histone deacetylation, or through sequestration of transcriptional activators. The product of this gene contains a carboxy-terminal domain that permits binding to other corepressor proteins. This domain also permits interaction with members of the NuRD complex, a nucleosome remodeling protein complex that contains deacetylase activity. In addition, this repressor contains several RNA recognition motifs that confer binding to a steroid receptor RNA coactivator; this binding can modulate the activity of both liganded and nonliganded steroid receptors. [provided by RefSeq, Jul 2008]

SPEN links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.0016164482).

BP6

Variant 1-15935976-A-C is Benign according to our data. Variant chr1-15935976-A-C is described in ClinVar as [Benign]. Clinvar id is 403486.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SPEN	NM_015001.3 link	c.9736A>C	p.Thr3246Pro	missense_variant	Exon 11 of 15	ENST00000375759.8	NP_055816.2	Q96T58

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	UniProt
SPEN	ENST00000375759.8 link	c.9736A>C	p.Thr3246Pro	missense_variant	Exon 11 of 15	1	NM_015001.3	ENSP00000364912.3	Q96T58
SPEN	ENST00000704274.1 link	c.5332A>C	p.Thr1778Pro	missense_variant	Exon 1 of 4			ENSP00000515812.1	A0A994J7B7
SPEN	ENST00000438066.2 link	n.*10587A>C		non_coding_transcript_exon_variant	Exon 11 of 15	3		ENSP00000388021.2	F6WRY4
SPEN	ENST00000438066.2 link	n.*10587A>C		3_prime_UTR_variant	Exon 11 of 15	3		ENSP00000388021.2	F6WRY4

Frequencies

GnomAD3 genomes

AF:

0.00

AC:

9353

AN:

39114

Hom.:

Cov.:

FAILED QC

Gnomad AFR

AF:

0.233

Gnomad AMI

AF:

0.192

Gnomad AMR

AF:

0.212

Gnomad ASJ

AF:

0.271

Gnomad EAS

AF:

0.160

Gnomad SAS

AF:

0.163

Gnomad FIN

AF:

0.155

Gnomad MID

AF:

0.0962

Gnomad NFE

AF:

0.271

Gnomad OTH

AF:

0.263

GnomAD4 exome

Data not reliable, filtered out with message: AS_VQSR

AF:

0.0679

AC:

22442

AN:

330518

Hom.:

Cov.:

AF XY:

0.0621

AC XY:

10592

AN XY:

170696

show subpopulations

Gnomad4 AFR exome

AF:

0.0446

Gnomad4 AMR exome

AF:

0.00706

Gnomad4 ASJ exome

AF:

0.0252

Gnomad4 EAS exome

AF:

0.0126

Gnomad4 SAS exome

AF:

0.0259

Gnomad4 FIN exome

AF:

0.0600

Gnomad4 NFE exome

AF:

0.0856

Gnomad4 OTH exome

AF:

0.0552

GnomAD4 genome

Data not reliable, filtered out with message: AS_VQSR;InbreedingCoeff

AF:

0.239

AC:

9356

AN:

39150

Hom.:

Cov.:

AF XY:

0.225

AC XY:

4295

AN XY:

19128

show subpopulations

Gnomad4 AFR

AF:

0.232

Gnomad4 AMR

AF:

0.213

Gnomad4 ASJ

AF:

0.271

Gnomad4 EAS

AF:

0.160

Gnomad4 SAS

AF:

0.161

Gnomad4 FIN

AF:

0.155

Gnomad4 NFE

AF:

0.271

Gnomad4 OTH

AF:

0.261

Alfa

AF:

0.0143

Hom.:

ExAC

AF:

0.0248

AC:

2869

ClinVar

Significance: Benign

Submissions summary: Benign:3

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not specified

Benign:1

Mar 29, 2016

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or databases. Disclaimer: This variant has not undergone full assessment. The following are preliminary notes: Fails ExAC quality filter -

not provided

Benign:1

Breakthrough Genomics, Breakthrough Genomics

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: not provided

- -

SPEN-related disorder

Benign:1

Mar 29, 2019

PreventionGenetics, part of Exact Sciences

Significance: Benign

Review Status: no assertion criteria provided

Collection Method: clinical testing

This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.086

BayesDel_addAF

Benign

-0.31

BayesDel_noAF

Benign

-0.68

CADD

Benign

0.075

DANN

Benign

0.14

DEOGEN2

Benign

0.16

Eigen

Benign

-1.7

Eigen_PC

Benign

-1.7

FATHMM_MKL

Benign

0.081

LIST_S2

Benign

0.26

MetaRNN

Benign

0.0016

MetaSVM

Benign

-0.95

MutationAssessor

Benign

-0.20

PrimateAI

Benign

0.43

PROVEAN

Benign

-0.44

REVEL

Benign

0.023

Sift

Benign

0.095

Sift4G

Benign

0.27

Polyphen

0.0

Vest4

0.028

MPC

0.30

ClinPred

0.000027

GERP RS

-0.92

Varity_R

0.057

gMVP

0.084

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