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GeneBe

10-116911832-C-T

Variant summary

Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BA1

The NM_001127211.3(SHTN1):c.1317G>A(p.Ser439=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00349 in 1,611,472 control chromosomes in the GnomAD database, including 166 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.019 ( 86 hom., cov: 33)
Exomes 𝑓: 0.0019 ( 80 hom. )

Consequence

SHTN1
NM_001127211.3 synonymous

Scores

2

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.144
Variant links:
Genes affected
SHTN1 (HGNC:29319): (shootin 1) Enables identical protein binding activity. Involved in positive regulation of neuron migration. Located in cytoplasm. [provided by Alliance of Genome Resources, Apr 2022]
ENO4 (HGNC:31670): (enolase 4) Predicted to enable phosphopyruvate hydratase activity. Predicted to be involved in glycolytic process and regulation of vacuole fusion, non-autophagic. Predicted to act upstream of or within cilium organization and flagellated sperm motility. Predicted to be located in sperm principal piece. Predicted to be part of phosphopyruvate hydratase complex. [provided by Alliance of Genome Resources, Apr 2022]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -15 ACMG points.

BP4
?
    BP4 - Multiple lines of computational evidence suggest no impact on gene or gene product (conservation, evolutionary, splicing impact, etc.)
Computational evidence support a benign effect (BayesDel_noAF=-0.47).
BP6
?
    BP6 - Reputable source recently reports variant as benign, but the evidence is not available to the laboratory to perform an independent evaluation
Variant 10-116911832-C-T is Benign according to our data. Variant chr10-116911832-C-T is described in ClinVar as [Benign]. Clinvar id is 768393.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
    BP7 - A synonymous (silent) variant for which splicing prediction algorithms predict no impact to the splice consensus sequence nor the creation of a new splice site AND the nucleotide is not highly conserved
Synonymous conserved (PhyloP=0.144 with no splicing effect.
BA1
?
    BA1 - Allele frequency is >5% in Exome Sequencing Project, 1000 Genomes Project, or Exome Aggregation Consortium
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.063 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
SHTN1NM_001127211.3 linkuse as main transcriptc.1317G>A p.Ser439= synonymous_variant 14/17 ENST00000355371.9

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
SHTN1ENST00000355371.9 linkuse as main transcriptc.1317G>A p.Ser439= synonymous_variant 14/172 NM_001127211.3 P1A0MZ66-1

Frequencies

GnomAD3 genomes
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.0190
AC:
2884
AN:
152110
Hom.:
86
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.0652
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00929
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.000207
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.000162
Gnomad OTH
AF:
0.0148
GnomAD3 exomes
AF:
0.00483
AC:
1213
AN:
250936
Hom.:
41
AF XY:
0.00349
AC XY:
474
AN XY:
135630
show subpopulations
Gnomad AFR exome
AF:
0.0639
Gnomad AMR exome
AF:
0.00420
Gnomad ASJ exome
AF:
0.0000993
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.0000327
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.0000794
Gnomad OTH exome
AF:
0.00311
GnomAD4 exome
AF:
0.00187
AC:
2733
AN:
1459244
Hom.:
80
Cov.:
29
AF XY:
0.00156
AC XY:
1132
AN XY:
726132
show subpopulations
Gnomad4 AFR exome
AF:
0.0649
Gnomad4 AMR exome
AF:
0.00501
Gnomad4 ASJ exome
AF:
0.000115
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.000255
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.0000784
Gnomad4 OTH exome
AF:
0.00375
GnomAD4 genome
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.0190
AC:
2885
AN:
152228
Hom.:
86
Cov.:
33
AF XY:
0.0179
AC XY:
1331
AN XY:
74418
show subpopulations
Gnomad4 AFR
AF:
0.0651
Gnomad4 AMR
AF:
0.00921
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.000207
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.000162
Gnomad4 OTH
AF:
0.0147
Alfa
AF:
0.00851
Hom.:
19
Bravo
AF:
0.0213
Asia WGS
AF:
0.00231
AC:
8
AN:
3476
EpiCase
AF:
0.000164
EpiControl
AF:
0.00

ClinVar

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

Submissions by phenotype

not provided Benign:1
Benign, criteria provided, single submitterclinical testingInvitaeJan 30, 2018- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.47
Cadd
Benign
7.3
Dann
Benign
0.81
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.7

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.020
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: rs62641722; hg19: chr10-118671343; API