14-55671640-C-T

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

Scores

2

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -2.68
Variant links:
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]

Genome browser will be placed here

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
KTN1NM_001079521.2 linkc.3423C>T p.Ser1141Ser synonymous_variant Exon 36 of 44 ENST00000395314.8 NP_001072989.1 Q86UP2-1A0A024R663

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
KTN1ENST00000395314.8 linkc.3423C>T p.Ser1141Ser synonymous_variant Exon 36 of 44 1 NM_001079521.2 ENSP00000378725.3 Q86UP2-1

Frequencies

GnomAD3 genomes
AF:
0.00773
AC:
1176
AN:
152076
Hom.:
7
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.00215
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00649
Gnomad ASJ
AF:
0.0121
Gnomad EAS
AF:
0.000385
Gnomad SAS
AF:
0.00601
Gnomad FIN
AF:
0.00755
Gnomad MID
AF:
0.00633
Gnomad NFE
AF:
0.0119
Gnomad OTH
AF:
0.0100
GnomAD3 exomes
AF:
0.00878
AC:
2188
AN:
249254
Hom.:
20
AF XY:
0.00917
AC XY:
1234
AN XY:
134612
show subpopulations
Gnomad AFR exome
AF:
0.00234
Gnomad AMR exome
AF:
0.00539
Gnomad ASJ exome
AF:
0.0134
Gnomad EAS exome
AF:
0.000328
Gnomad SAS exome
AF:
0.00522
Gnomad FIN exome
AF:
0.00810
Gnomad NFE exome
AF:
0.0127
Gnomad OTH exome
AF:
0.00955
GnomAD4 exome
AF:
0.0109
AC:
15937
AN:
1458424
Hom.:
109
Cov.:
29
AF XY:
0.0108
AC XY:
7848
AN XY:
725552
show subpopulations
Gnomad4 AFR exome
AF:
0.00174
Gnomad4 AMR exome
AF:
0.00538
Gnomad4 ASJ exome
AF:
0.0134
Gnomad4 EAS exome
AF:
0.000227
Gnomad4 SAS exome
AF:
0.00563
Gnomad4 FIN exome
AF:
0.00787
Gnomad4 NFE exome
AF:
0.0124
Gnomad4 OTH exome
AF:
0.0103
GnomAD4 genome
AF:
0.00773
AC:
1176
AN:
152194
Hom.:
7
Cov.:
32
AF XY:
0.00722
AC XY:
537
AN XY:
74422
show subpopulations
Gnomad4 AFR
AF:
0.00214
Gnomad4 AMR
AF:
0.00648
Gnomad4 ASJ
AF:
0.0121
Gnomad4 EAS
AF:
0.000386
Gnomad4 SAS
AF:
0.00601
Gnomad4 FIN
AF:
0.00755
Gnomad4 NFE
AF:
0.0119
Gnomad4 OTH
AF:
0.00992
Alfa
AF:
0.0102
Hom.:
3
Bravo
AF:
0.00736
Asia WGS
AF:
0.00202
AC:
7
AN:
3476
EpiCase
AF:
0.0119
EpiControl
AF:
0.0143

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

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.54
CADD
Benign
5.9
DANN
Benign
0.54
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.7

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.10
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: rs41304375; hg19: chr14-56138358; COSMIC: COSV58540282; COSMIC: COSV58540282; API