rs10412199

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_033064.5(ATCAY):​c.*3181G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.389 in 152,180 control chromosomes in the GnomAD database, including 12,023 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.39 ( 12010 hom., cov: 32)
Exomes 𝑓: 0.52 ( 13 hom. )

Consequence

ATCAY
NM_033064.5 3_prime_UTR

Scores

2

Clinical Significance

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

Conservation

PhyloP100: -2.64
Variant links:
Genes affected
ATCAY (HGNC:779): (ATCAY kinesin light chain interacting caytaxin) This gene encodes a neuron-restricted protein that contains a CRAL-TRIO motif common to proteins that bind small lipophilic molecules. Mutations in this gene are associated with cerebellar ataxia, Cayman type. [provided by RefSeq, Jul 2008]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.98).
BP6
Variant 19-3927773-G-A is Benign according to our data. Variant chr19-3927773-G-A is described in ClinVar as [Benign]. Clinvar id is 329202.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.598 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
ATCAYNM_033064.5 linkc.*3181G>A 3_prime_UTR_variant Exon 13 of 13 ENST00000450849.7 NP_149053.1 Q86WG3-1A0A0S2Z5T8
ATCAYXM_047439578.1 linkc.*3181G>A 3_prime_UTR_variant Exon 12 of 12 XP_047295534.1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
ATCAYENST00000450849.7 linkc.*3181G>A 3_prime_UTR_variant Exon 13 of 13 1 NM_033064.5 ENSP00000390941.1 Q86WG3-1

Frequencies

GnomAD3 genomes
AF:
0.389
AC:
59088
AN:
151958
Hom.:
11991
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.397
Gnomad AMI
AF:
0.341
Gnomad AMR
AF:
0.494
Gnomad ASJ
AF:
0.391
Gnomad EAS
AF:
0.569
Gnomad SAS
AF:
0.616
Gnomad FIN
AF:
0.335
Gnomad MID
AF:
0.497
Gnomad NFE
AF:
0.338
Gnomad OTH
AF:
0.409
GnomAD4 exome
AF:
0.519
AC:
54
AN:
104
Hom.:
13
Cov.:
0
AF XY:
0.487
AC XY:
39
AN XY:
80
show subpopulations
Gnomad4 AFR exome
AF:
0.250
Gnomad4 AMR exome
AF:
0.500
Gnomad4 FIN exome
AF:
0.750
Gnomad4 NFE exome
AF:
0.533
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
AF:
0.389
AC:
59141
AN:
152076
Hom.:
12010
Cov.:
32
AF XY:
0.397
AC XY:
29483
AN XY:
74348
show subpopulations
Gnomad4 AFR
AF:
0.397
Gnomad4 AMR
AF:
0.495
Gnomad4 ASJ
AF:
0.391
Gnomad4 EAS
AF:
0.568
Gnomad4 SAS
AF:
0.616
Gnomad4 FIN
AF:
0.335
Gnomad4 NFE
AF:
0.338
Gnomad4 OTH
AF:
0.406
Alfa
AF:
0.361
Hom.:
15621
Bravo
AF:
0.398
Asia WGS
AF:
0.602
AC:
2088
AN:
3478

ClinVar

Significance: Benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link

Submissions by phenotype

Cayman type cerebellar ataxia Benign:1
Jan 13, 2018
Illumina Laboratory Services, Illumina
Significance: Benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing

This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. -

not provided Benign:1
-
Breakthrough Genomics, Breakthrough Genomics
Significance: Benign
Review Status: criteria provided, single submitter
Collection Method: not provided

- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.98
CADD
Benign
0.12
DANN
Benign
0.53

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: rs10412199; hg19: chr19-3927771; API