2-179116713-C-T
Variant names:
Variant summary
Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_ModerateBP6_Very_StrongBP7BS2
The NM_178123.5(SESTD1):c.1602G>A(p.Thr534Thr) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00197 in 1,614,096 control chromosomes in the GnomAD database, including 6 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.0018 ( 0 hom., cov: 32)
Exomes 𝑓: 0.0020 ( 6 hom. )
Consequence
SESTD1
NM_178123.5 synonymous
NM_178123.5 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.853
Genes affected
SESTD1 (HGNC:18379): (SEC14 and spectrin domain containing 1) Enables phosphatidylinositol-3,4-bisphosphate binding activity and phospholipid binding activity. Involved in negative regulation of calcium ion transmembrane transport via high voltage-gated calcium channel. Located in intermediate filament cytoskeleton. Colocalizes with calcium channel 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
Computational evidence support a benign effect (BayesDel_noAF=-0.26).
BP6
Variant 2-179116713-C-T is Benign according to our data. Variant chr2-179116713-C-T is described in ClinVar as [Benign]. Clinvar id is 770877.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BP7
Synonymous conserved (PhyloP=-0.853 with no splicing effect.
BS2
High AC in GnomAd4 at 267 AD gene.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SESTD1 | ENST00000428443.8 | c.1602G>A | p.Thr534Thr | synonymous_variant | Exon 15 of 18 | 1 | NM_178123.5 | ENSP00000415332.2 | ||
SESTD1 | ENST00000335289.5 | n.*319G>A | non_coding_transcript_exon_variant | Exon 7 of 10 | 5 | ENSP00000334183.5 | ||||
SESTD1 | ENST00000446758.5 | n.537G>A | non_coding_transcript_exon_variant | Exon 5 of 8 | 2 | ENSP00000410632.1 | ||||
SESTD1 | ENST00000335289.5 | n.*319G>A | 3_prime_UTR_variant | Exon 7 of 10 | 5 | ENSP00000334183.5 |
Frequencies
GnomAD3 genomes AF: 0.00175 AC: 267AN: 152188Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.00197 AC: 495AN: 251200Hom.: 1 AF XY: 0.00194 AC XY: 264AN XY: 135760
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GnomAD4 exome AF: 0.00200 AC: 2918AN: 1461790Hom.: 6 Cov.: 31 AF XY: 0.00195 AC XY: 1420AN XY: 727200
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GnomAD4 genome AF: 0.00175 AC: 267AN: 152306Hom.: 0 Cov.: 32 AF XY: 0.00187 AC XY: 139AN XY: 74478
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ClinVar
Significance: Benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:2
Jul 31, 2018
Labcorp Genetics (formerly Invitae), Labcorp
Significance: Benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing
- -
-
Breakthrough Genomics, Breakthrough Genomics
Significance: Benign
Review Status: criteria provided, single submitter
Collection Method: not provided
- -
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at