chr17-5014050-G-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_006612.6(KIF1C):​c.1571+318G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0548 in 332,192 control chromosomes in the GnomAD database, including 766 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.048 ( 237 hom., cov: 32)
Exomes 𝑓: 0.061 ( 529 hom. )

Consequence

KIF1C
NM_006612.6 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.539
Variant links:
Genes affected
KIF1C (HGNC:6317): (kinesin family member 1C) The protein encoded by this gene is a member of the kinesin-like protein family. The family members are microtubule-dependent molecular motors that transport organelles within cells and move chromosomes during cell division. Mutations in this gene are a cause of spastic ataxia 2, autosomal recessive. [provided by RefSeq, May 2014]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.92).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.189 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
KIF1CNM_006612.6 linkuse as main transcriptc.1571+318G>C intron_variant ENST00000320785.10 NP_006603.2
KIF1CXM_005256424.3 linkuse as main transcriptc.1571+318G>C intron_variant XP_005256481.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
KIF1CENST00000320785.10 linkuse as main transcriptc.1571+318G>C intron_variant 1 NM_006612.6 ENSP00000320821 P1

Frequencies

GnomAD3 genomes
AF:
0.0480
AC:
7298
AN:
152172
Hom.:
238
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0367
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.0413
Gnomad ASJ
AF:
0.0536
Gnomad EAS
AF:
0.199
Gnomad SAS
AF:
0.0992
Gnomad FIN
AF:
0.0254
Gnomad MID
AF:
0.0506
Gnomad NFE
AF:
0.0449
Gnomad OTH
AF:
0.0516
GnomAD4 exome
AF:
0.0607
AC:
10920
AN:
179902
Hom.:
529
AF XY:
0.0618
AC XY:
5749
AN XY:
93054
show subpopulations
Gnomad4 AFR exome
AF:
0.0389
Gnomad4 AMR exome
AF:
0.0402
Gnomad4 ASJ exome
AF:
0.0685
Gnomad4 EAS exome
AF:
0.230
Gnomad4 SAS exome
AF:
0.0869
Gnomad4 FIN exome
AF:
0.0316
Gnomad4 NFE exome
AF:
0.0459
Gnomad4 OTH exome
AF:
0.0552
GnomAD4 genome
AF:
0.0479
AC:
7291
AN:
152290
Hom.:
237
Cov.:
32
AF XY:
0.0490
AC XY:
3647
AN XY:
74470
show subpopulations
Gnomad4 AFR
AF:
0.0367
Gnomad4 AMR
AF:
0.0413
Gnomad4 ASJ
AF:
0.0536
Gnomad4 EAS
AF:
0.199
Gnomad4 SAS
AF:
0.0980
Gnomad4 FIN
AF:
0.0254
Gnomad4 NFE
AF:
0.0449
Gnomad4 OTH
AF:
0.0501
Alfa
AF:
0.0463
Hom.:
17
Bravo
AF:
0.0490
Asia WGS
AF:
0.127
AC:
442
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.92
CADD
Benign
0.12
DANN
Benign
0.54

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: rs376647; hg19: chr17-4917345; COSMIC: COSV57903613; COSMIC: COSV57903613; API