X-143629567-G-A

Variant summary

Our verdict is Benign. Variant got -7 ACMG points: 0P and 7B. BP4_StrongBP6_ModerateBP7

The NM_001184749.3(SLITRK4):​c.1542C>T​(p.Ser514Ser) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.87 ( 30818 hom., 28193 hem., cov: 22)
Exomes 𝑓: 0.99 ( 357894 hom. 359386 hem. )
Failed GnomAD Quality Control

Consequence

SLITRK4
NM_001184749.3 synonymous

Scores

1

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.0630
Variant links:
Genes affected
SLITRK4 (HGNC:23502): (SLIT and NTRK like family member 4) This gene encodes a transmembrane protein belonging to the the SLITRK family. These family members include two N-terminal leucine-rich repeat domains similar to those found in the axonal growth-controlling protein SLIT, as well as C-terminal regions similar to neurotrophin receptors. Studies of an homologous protein in mouse suggest that this family member functions to suppress neurite outgrowth. Alternative splicing results in multiple transcript variants. [provided by RefSeq, May 2010]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -7 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.51).
BP6
Variant X-143629567-G-A is Benign according to our data. Variant chrX-143629567-G-A is described in ClinVar as [Benign]. Clinvar id is 769233.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=0.063 with no splicing effect.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
SLITRK4NM_001184749.3 linkc.1542C>T p.Ser514Ser synonymous_variant Exon 2 of 2 ENST00000356928.2 NP_001171678.1 Q8IW52

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
SLITRK4ENST00000356928.2 linkc.1542C>T p.Ser514Ser synonymous_variant Exon 2 of 2 2 NM_001184749.3 ENSP00000349400.1 Q8IW52
SLITRK4ENST00000338017.8 linkc.1542C>T p.Ser514Ser synonymous_variant Exon 2 of 2 1 ENSP00000336627.4 Q8IW52
SLITRK4ENST00000596188.2 linkc.1542C>T p.Ser514Ser synonymous_variant Exon 2 of 2 1 ENSP00000469205.1 Q8IW52

Frequencies

GnomAD3 genomes
AF:
0.872
AC:
95698
AN:
109752
Hom.:
30823
Cov.:
22
AF XY:
0.880
AC XY:
28150
AN XY:
31988
show subpopulations
Gnomad AFR
AF:
0.561
Gnomad AMI
AF:
1.00
Gnomad AMR
AF:
0.940
Gnomad ASJ
AF:
0.999
Gnomad EAS
AF:
1.00
Gnomad SAS
AF:
0.998
Gnomad FIN
AF:
1.00
Gnomad MID
AF:
0.979
Gnomad NFE
AF:
0.998
Gnomad OTH
AF:
0.898
GnomAD4 exome
Data not reliable, filtered out with message: InbreedingCoeff
AF:
0.986
AC:
1082492
AN:
1098252
Hom.:
357894
Cov.:
65
AF XY:
0.988
AC XY:
359386
AN XY:
363606
show subpopulations
Gnomad4 AFR exome
AF:
0.547
Gnomad4 AMR exome
AF:
0.972
Gnomad4 ASJ exome
AF:
0.998
Gnomad4 EAS exome
AF:
1.00
Gnomad4 SAS exome
AF:
0.999
Gnomad4 FIN exome
AF:
1.00
Gnomad4 NFE exome
AF:
0.999
Gnomad4 OTH exome
AF:
0.966
GnomAD4 genome
Data not reliable, filtered out with message: InbreedingCoeff
AF:
0.872
AC:
95731
AN:
109801
Hom.:
30818
Cov.:
22
AF XY:
0.880
AC XY:
28193
AN XY:
32047
show subpopulations
Gnomad4 AFR
AF:
0.562
Gnomad4 AMR
AF:
0.940
Gnomad4 ASJ
AF:
0.999
Gnomad4 EAS
AF:
1.00
Gnomad4 SAS
AF:
0.998
Gnomad4 FIN
AF:
1.00
Gnomad4 NFE
AF:
0.998
Gnomad4 OTH
AF:
0.899
Alfa
AF:
0.946
Hom.:
13799
Bravo
AF:
0.852

ClinVar

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

Submissions by phenotype

not provided Benign:1
Aug 16, 2017
Labcorp Genetics (formerly Invitae), Labcorp
Significance: Benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.51
CADD
Benign
0.55

Splicing

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: rs73577386; hg19: chrX-142717383; API