GeneBe

chr2-98821958-G-A

Variant names:

Variant summary

Our verdict is Likely benign. The variant received -1 ACMG points: 0P and 1B. BP4

The NM_207362.3(CRACDL):​c.2315C>T​(p.Thr772Met) variant causes a missense change. The variant allele was found at a frequency of 0.000068 in 1,544,864 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: 𝑓 0.00017 ( 0 hom., cov: 32)
Exomes 𝑓: 0.000057 ( 0 hom. )

Consequence

CRACDL
NM_207362.3 missense

Scores

9
10

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 4.37
Variant links:
Genes affected
CRACDL (HGNC:33454): (CRACD like)

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Likely_benign. The variant received -1 ACMG points.

BP4
Computational evidence support a benign effect (MetaRNN=0.26846242).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
CRACDLNM_207362.3 linkc.2315C>T p.Thr772Met missense_variant Exon 7 of 10 ENST00000397899.7 NP_997245.2

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
CRACDLENST00000397899.7 linkc.2315C>T p.Thr772Met missense_variant Exon 7 of 10 1 NM_207362.3 ENSP00000380996.2 Q6NV74
CRACDLENST00000464413.1 linkn.347C>T non_coding_transcript_exon_variant Exon 1 of 2 3

Frequencies

GnomAD3 genomes
AF:
0.000171
AC:
26
AN:
152108
Hom.:
0
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.000410
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.000131
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.0000882
Gnomad OTH
AF:
0.000478
GnomAD2 exomes
AF:
0.0000421
AC:
6
AN:
142452
AF XY:
0.0000257
show subpopulations
Gnomad AFR exome
AF:
0.000295
Gnomad AMR exome
AF:
0.00
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.0000537
Gnomad OTH exome
AF:
0.000260
GnomAD4 exome
AF:
0.0000567
AC:
79
AN:
1392638
Hom.:
0
Cov.:
33
AF XY:
0.0000596
AC XY:
41
AN XY:
688180
show subpopulations
African (AFR)
AF:
0.000197
AC:
6
AN:
30406
American (AMR)
AF:
0.0000299
AC:
1
AN:
33402
Ashkenazi Jewish (ASJ)
AF:
0.00
AC:
0
AN:
24468
East Asian (EAS)
AF:
0.00
AC:
0
AN:
35776
South Asian (SAS)
AF:
0.00
AC:
0
AN:
78800
European-Finnish (FIN)
AF:
0.00
AC:
0
AN:
47466
Middle Eastern (MID)
AF:
0.00
AC:
0
AN:
5408
European-Non Finnish (NFE)
AF:
0.0000667
AC:
72
AN:
1079474
Other (OTH)
AF:
0.00
AC:
0
AN:
57438
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.483
Heterozygous variant carriers
0
4
9
13
18
22
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Exome Het
Variant carriers
0
4
8
12
16
20
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
GnomAD4 genome
AF:
0.000171
AC:
26
AN:
152226
Hom.:
0
Cov.:
32
AF XY:
0.000202
AC XY:
15
AN XY:
74440
show subpopulations
African (AFR)
AF:
0.000409
AC:
17
AN:
41556
American (AMR)
AF:
0.000131
AC:
2
AN:
15290
Ashkenazi Jewish (ASJ)
AF:
0.00
AC:
0
AN:
3470
East Asian (EAS)
AF:
0.00
AC:
0
AN:
5166
South Asian (SAS)
AF:
0.00
AC:
0
AN:
4820
European-Finnish (FIN)
AF:
0.00
AC:
0
AN:
10612
Middle Eastern (MID)
AF:
0.00
AC:
0
AN:
294
European-Non Finnish (NFE)
AF:
0.0000882
AC:
6
AN:
67990
Other (OTH)
AF:
0.000473
AC:
1
AN:
2116
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.458
Heterozygous variant carriers
0
2
3
5
6
8
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Variant carriers
0
2
4
6
8
10
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
Alfa
AF:
0.000170
Hom.:
0
Bravo
AF:
0.000196
ESP6500AA
AF:
0.000588
AC:
2
ESP6500EA
AF:
0.00
AC:
0
ExAC
AF:
0.0000358
AC:
4

ClinVar

Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not specified Uncertain:1
Sep 07, 2022
Ambry Genetics
Significance:Uncertain significance
Review Status:criteria provided, single submitter
Collection Method:clinical testing

The c.2315C>T (p.T772M) alteration is located in exon 7 (coding exon 6) of the KIAA1211L gene. This alteration results from a C to T substitution at nucleotide position 2315, causing the threonine (T) at amino acid position 772 to be replaced by a methionine (M). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.18
BayesDel_addAF
Benign
-0.22
T
BayesDel_noAF
Benign
-0.31
CADD
Pathogenic
26
DANN
Uncertain
0.99
DEOGEN2
Benign
0.19
T
Eigen
Uncertain
0.51
Eigen_PC
Uncertain
0.43
FATHMM_MKL
Uncertain
0.91
D
LIST_S2
Benign
0.77
T
M_CAP
Uncertain
0.086
D
MetaRNN
Benign
0.27
T
MetaSVM
Benign
-0.61
T
MutationAssessor
Uncertain
2.6
M
PhyloP100
4.4
PrimateAI
Uncertain
0.58
T
PROVEAN
Uncertain
-3.6
D
REVEL
Benign
0.20
Sift
Uncertain
0.0050
D
Sift4G
Benign
0.061
T
Polyphen
1.0
D
Vest4
0.18
MVP
0.24
ClinPred
0.66
D
GERP RS
4.8
Varity_R
0.13
gMVP
0.30
Mutation Taster
=95/5
polymorphism

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 for variant 2:98821958 G>A . It may be empty.

Other links and lift over

dbSNP: rs150915151; hg19: chr2-99438421; API