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GeneBe

8-144466443-C-T

Variant summary

Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BS1BS2

The NM_001369769.2(KIFC2):c.24C>T(p.Leu8=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00172 in 1,363,372 control chromosomes in the GnomAD database, including 30 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.0028 ( 1 hom., cov: 30)
Exomes 𝑓: 0.0016 ( 29 hom. )

Consequence

KIFC2
NM_001369769.2 synonymous

Scores

2

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.0820
Variant links:
Genes affected
KIFC2 (HGNC:29530): (kinesin family member C2) Predicted to enable microtubule binding activity and microtubule motor activity. Predicted to be involved in microtubule-based movement and mitotic spindle assembly. Predicted to be located in cytoplasm. Predicted to be part of kinesin complex. Predicted to be active in microtubule cytoskeleton and nucleus. [provided by Alliance of Genome Resources, Apr 2022]

Genome browser will be placed here

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=-0.59).
BP6
?
    BP6 - Reputable source recently reports variant as benign, but the evidence is not available to the laboratory to perform an independent evaluation
Variant 8-144466443-C-T is Benign according to our data. Variant chr8-144466443-C-T is described in ClinVar as [Benign]. Clinvar id is 782144.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=-0.082 with no splicing effect.
BS1
?
    BS1 - Allele frequency is greater than expected for disorder
Variant frequency is greater than expected in population sas. gnomad4 allele frequency = 0.00278 (417/150082) while in subpopulation SAS AF= 0.0193 (93/4814). AF 95% confidence interval is 0.0161. There are 1 homozygotes in gnomad4. There are 223 alleles in male gnomad4 subpopulation. Median coverage is 30. This position pass quality control queck.
BS2
?
    BS2 - Observed in a healthy adult individual for a recessive (homozygous), dominant (heterozygous), or X-linked (hemizygous) disorder, with full penetrance expected at an early age
High Homozygotes in GnomAdExome at 7 gene

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
KIFC2NM_001369769.2 linkuse as main transcriptc.24C>T p.Leu8= synonymous_variant 1/18 ENST00000645548.2
TMEM276NM_001408062.1 linkuse as main transcriptc.-196+510G>A intron_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
KIFC2ENST00000645548.2 linkuse as main transcriptc.24C>T p.Leu8= synonymous_variant 1/18 NM_001369769.2 P1
KIFC2ENST00000301332.3 linkuse as main transcriptc.24C>T p.Leu8= synonymous_variant 1/171 Q96AC6-1
KIFC2ENST00000642354.1 linkuse as main transcriptc.24C>T p.Leu8= synonymous_variant 1/18
KIFC2ENST00000643461.1 linkuse as main transcriptn.401C>T non_coding_transcript_exon_variant 1/17

Frequencies

GnomAD3 genomes
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.00272
AC:
408
AN:
149974
Hom.:
1
Cov.:
30
show subpopulations
Gnomad AFR
AF:
0.00450
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00384
Gnomad ASJ
AF:
0.000290
Gnomad EAS
AF:
0.00216
Gnomad SAS
AF:
0.0191
Gnomad FIN
AF:
0.000101
Gnomad MID
AF:
0.0191
Gnomad NFE
AF:
0.000670
Gnomad OTH
AF:
0.00436
GnomAD3 exomes
AF:
0.00350
AC:
488
AN:
139430
Hom.:
7
AF XY:
0.00434
AC XY:
349
AN XY:
80352
show subpopulations
Gnomad AFR exome
AF:
0.00280
Gnomad AMR exome
AF:
0.00144
Gnomad ASJ exome
AF:
0.000146
Gnomad EAS exome
AF:
0.000150
Gnomad SAS exome
AF:
0.0201
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.000673
Gnomad OTH exome
AF:
0.00336
GnomAD4 exome
AF:
0.00159
AC:
1933
AN:
1213290
Hom.:
29
Cov.:
29
AF XY:
0.00190
AC XY:
1140
AN XY:
600682
show subpopulations
Gnomad4 AFR exome
AF:
0.00463
Gnomad4 AMR exome
AF:
0.00163
Gnomad4 ASJ exome
AF:
0.000110
Gnomad4 EAS exome
AF:
0.00246
Gnomad4 SAS exome
AF:
0.0190
Gnomad4 FIN exome
AF:
0.0000263
Gnomad4 NFE exome
AF:
0.000487
Gnomad4 OTH exome
AF:
0.00286
GnomAD4 genome
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.00278
AC:
417
AN:
150082
Hom.:
1
Cov.:
30
AF XY:
0.00304
AC XY:
223
AN XY:
73310
show subpopulations
Gnomad4 AFR
AF:
0.00458
Gnomad4 AMR
AF:
0.00383
Gnomad4 ASJ
AF:
0.000290
Gnomad4 EAS
AF:
0.00217
Gnomad4 SAS
AF:
0.0193
Gnomad4 FIN
AF:
0.000101
Gnomad4 NFE
AF:
0.000670
Gnomad4 OTH
AF:
0.00671
Alfa
AF:
0.000156
Hom.:
0
Asia WGS
AF:
0.0180
AC:
59
AN:
3172

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 testingInvitaeJun 28, 2017- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.59
Cadd
Benign
12
Dann
Benign
0.93

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.16
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: rs142310829; hg19: chr8-145691826; API