X-143629567-G-A

Variant names:

• chrX-143629567-G-A
• rs73577386
• NM_001184749.3:c.1542C>T

Variant summary

Our verdict is Benign. Variant got -7 ACMG points: 0P and 7B. BP4_Strong BP6_Moderate BP7

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
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.0630

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]

ACMG classification

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
SLITRK4	NM_001184749.3	c.1542C>T	p.Ser514Ser	synonymous_variant	Exon 2 of 2	ENST00000356928.2	NP_001171678.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLITRK4	ENST00000356928.2	c.1542C>T	p.Ser514Ser	synonymous_variant	Exon 2 of 2	2	NM_001184749.3	ENSP00000349400.1
SLITRK4	ENST00000338017.8	c.1542C>T	p.Ser514Ser	synonymous_variant	Exon 2 of 2	1		ENSP00000336627.4
SLITRK4	ENST00000596188.2	c.1542C>T	p.Ser514Ser	synonymous_variant	Exon 2 of 2	1		ENSP00000469205.1

Frequencies

GnomAD3 genomes AF: 0.872 AC: 95698 AN: 109752 Hom.: 30823 Cov.: 22 AF XY: 0.880 AC XY: 28150 AN XY: 31988

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

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

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

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

Other links and lift over

dbSNP: rs73577386; hg19: chrX-142717383;