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11-117187689-C-T

Variant summary

Our verdict is Likely benign. Variant got -5 ACMG points: 2P and 7B. PM2BP4_StrongBP6_ModerateBP7

The NM_001040455.2(SIDT2):c.1149C>T(p.Tyr383=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00113 in 1,613,778 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.0015 ( 0 hom., cov: 31)
Exomes 𝑓: 0.0011 ( 1 hom. )

Consequence

SIDT2
NM_001040455.2 synonymous

Scores

2

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.187
Variant links:
Genes affected
SIDT2 (HGNC:24272): (SID1 transmembrane family member 2) Predicted to enable several functions, including AP-1 adaptor complex binding activity; AP-2 adaptor complex binding activity; and RNA transmembrane transporter activity. Involved in RNA transport. Located in lysosomal membrane and plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -5 ACMG points.

PM2
?
    PM2 - Absent from controls (or at extremely low frequency if recessive) in Exome Sequencing Project, 1000 Genomes Project, or Exome Aggregation Consortium
Very rare variant in population databases, with high coverage;
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=-0.65).
BP6
?
    BP6 - Reputable source recently reports variant as benign, but the evidence is not available to the laboratory to perform an independent evaluation
Variant 11-117187689-C-T is Benign according to our data. Variant chr11-117187689-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 2642404.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=-0.187 with no splicing effect.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
SIDT2NM_001040455.2 linkuse as main transcriptc.1149C>T p.Tyr383= synonymous_variant 12/26 ENST00000324225.9

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
SIDT2ENST00000324225.9 linkuse as main transcriptc.1149C>T p.Tyr383= synonymous_variant 12/261 NM_001040455.2 P3Q8NBJ9-1

Frequencies

GnomAD3 genomes
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.00143
AC:
217
AN:
151880
Hom.:
0
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.000895
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.0000657
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00852
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.00124
Gnomad OTH
AF:
0.00240
GnomAD3 exomes
AF:
0.00161
AC:
404
AN:
251472
Hom.:
1
AF XY:
0.00155
AC XY:
210
AN XY:
135914
show subpopulations
Gnomad AFR exome
AF:
0.000861
Gnomad AMR exome
AF:
0.0000578
Gnomad ASJ exome
AF:
0.0000992
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.0000980
Gnomad FIN exome
AF:
0.00989
Gnomad NFE exome
AF:
0.00135
Gnomad OTH exome
AF:
0.00261
GnomAD4 exome
AF:
0.00109
AC:
1595
AN:
1461780
Hom.:
1
Cov.:
31
AF XY:
0.00111
AC XY:
805
AN XY:
727214
show subpopulations
Gnomad4 AFR exome
AF:
0.000896
Gnomad4 AMR exome
AF:
0.0000671
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.0000464
Gnomad4 FIN exome
AF:
0.00914
Gnomad4 NFE exome
AF:
0.000868
Gnomad4 OTH exome
AF:
0.00171
GnomAD4 genome
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.00145
AC:
221
AN:
151998
Hom.:
0
Cov.:
31
AF XY:
0.00171
AC XY:
127
AN XY:
74270
show subpopulations
Gnomad4 AFR
AF:
0.000989
Gnomad4 AMR
AF:
0.0000656
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00852
Gnomad4 NFE
AF:
0.00124
Gnomad4 OTH
AF:
0.00237
Alfa
AF:
0.00123
Hom.:
0
Bravo
AF:
0.000790
Asia WGS
AF:
0.000577
AC:
2
AN:
3478
EpiCase
AF:
0.00115
EpiControl
AF:
0.000593

ClinVar

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

Submissions by phenotype

not provided Benign:1
Likely benign, criteria provided, single submitterclinical testingCeGaT Center for Human Genetics TuebingenJan 01, 2023SIDT2: BP4, BP7 -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.65
Cadd
Benign
7.5
Dann
Benign
0.35
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.1

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: rs148750007; hg19: chr11-117058405; API