14-55671640-C-T
Variant names:
Variant summary
Our verdict is Benign. Variant got -17 ACMG points: 0P and 17B. BP4_StrongBP6_Very_StrongBP7BS2
The NM_001079521.2(KTN1):c.3423C>T(p.Ser1141Ser) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0106 in 1,610,618 control chromosomes in the GnomAD database, including 116 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.0077 ( 7 hom., cov: 32)
Exomes 𝑓: 0.011 ( 109 hom. )
Consequence
KTN1
NM_001079521.2 synonymous
NM_001079521.2 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -2.68
Genes affected
KTN1 (HGNC:6467): (kinectin 1) This gene encodes an integral membrane protein that is a member of the kinectin protein family. The encoded protein is primarily localized to the endoplasmic reticulum membrane. This protein binds kinesin and may be involved in intracellular organelle motility. This protein also binds translation elongation factor-delta and may be involved in the assembly of the elongation factor-1 complex. Alternate splicing results in multiple transcript variants of this gene. [provided by RefSeq, Aug 2012]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -17 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.54).
BP6
Variant 14-55671640-C-T is Benign according to our data. Variant chr14-55671640-C-T is described in ClinVar as [Benign]. Clinvar id is 768655.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BP7
Synonymous conserved (PhyloP=-2.68 with no splicing effect.
BS2
High Homozygotes in GnomAd4 at 7 gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
KTN1 | NM_001079521.2 | c.3423C>T | p.Ser1141Ser | synonymous_variant | Exon 36 of 44 | ENST00000395314.8 | NP_001072989.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00773 AC: 1176AN: 152076Hom.: 7 Cov.: 32
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GnomAD3 exomes AF: 0.00878 AC: 2188AN: 249254Hom.: 20 AF XY: 0.00917 AC XY: 1234AN XY: 134612
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GnomAD4 exome AF: 0.0109 AC: 15937AN: 1458424Hom.: 109 Cov.: 29 AF XY: 0.0108 AC XY: 7848AN XY: 725552
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GnomAD4 genome AF: 0.00773 AC: 1176AN: 152194Hom.: 7 Cov.: 32 AF XY: 0.00722 AC XY: 537AN XY: 74422
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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
-
Breakthrough Genomics, Breakthrough Genomics
Significance: Benign
Review Status: criteria provided, single submitter
Collection Method: not provided
- -
Feb 25, 2018
Labcorp Genetics (formerly Invitae), Labcorp
Significance: Benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing
- -
Computational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
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