chr8-50500031-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_018967.5(SNTG1):​c.364-2747C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.725 in 151,782 control chromosomes in the GnomAD database, including 41,470 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.72 ( 41470 hom., cov: 31)

Consequence

SNTG1
NM_018967.5 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.409
Variant links:
Genes affected
SNTG1 (HGNC:13740): (syntrophin gamma 1) The protein encoded by this gene is a member of the syntrophin family. Syntrophins are cytoplasmic peripheral membrane proteins that typically contain 2 pleckstrin homology (PH) domains, a PDZ domain that bisects the first PH domain, and a C-terminal domain that mediates dystrophin binding. This family member plays a role in mediating gamma-enolase trafficking to the plasma membrane and in enhancing its neurotrophic activity. Mutations in this gene are associated with idiopathic scoliosis. Alternatively spliced transcript variants have been found for this gene. [provided by RefSeq, Mar 2016]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-1.0).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.824 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
SNTG1NM_018967.5 linkuse as main transcriptc.364-2747C>T intron_variant ENST00000642720.2 NP_061840.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
SNTG1ENST00000642720.2 linkuse as main transcriptc.364-2747C>T intron_variant NM_018967.5 ENSP00000493900 P1Q9NSN8-1

Frequencies

GnomAD3 genomes
AF:
0.725
AC:
109961
AN:
151664
Hom.:
41462
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.498
Gnomad AMI
AF:
0.855
Gnomad AMR
AF:
0.758
Gnomad ASJ
AF:
0.795
Gnomad EAS
AF:
0.846
Gnomad SAS
AF:
0.751
Gnomad FIN
AF:
0.786
Gnomad MID
AF:
0.697
Gnomad NFE
AF:
0.830
Gnomad OTH
AF:
0.740
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.725
AC:
110018
AN:
151782
Hom.:
41470
Cov.:
31
AF XY:
0.723
AC XY:
53661
AN XY:
74186
show subpopulations
Gnomad4 AFR
AF:
0.498
Gnomad4 AMR
AF:
0.758
Gnomad4 ASJ
AF:
0.795
Gnomad4 EAS
AF:
0.845
Gnomad4 SAS
AF:
0.753
Gnomad4 FIN
AF:
0.786
Gnomad4 NFE
AF:
0.830
Gnomad4 OTH
AF:
0.741
Alfa
AF:
0.817
Hom.:
61126
Bravo
AF:
0.714
Asia WGS
AF:
0.782
AC:
2700
AN:
3456

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-1.0
CADD
Benign
1.0
DANN
Benign
0.65

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.

Other links and lift over

dbSNP: rs310558; hg19: chr8-51412591; API