chr17-44962350-T-A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_006688.5(C1QL1):​c.598-1983A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.314 in 152,090 control chromosomes in the GnomAD database, including 8,264 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 0.31 ( 8264 hom., cov: 32)

Consequence

C1QL1
NM_006688.5 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0240

Publications

2 publications found
Variant links:
Genes affected
C1QL1 (HGNC:24182): (complement C1q like 1) Predicted to enable signaling receptor binding activity. Predicted to act upstream of or within maintenance of synapse structure; motor learning; and neuron remodeling. Predicted to be located in several cellular components, including climbing fiber; presynapse; and synaptic cleft. Predicted to be part of collagen trimer. [provided by Alliance of Genome Resources, Apr 2022]
NMT1 (HGNC:7857): (N-myristoyltransferase 1) Myristate, a rare 14-carbon saturated fatty acid, is cotranslationally attached by an amide linkage to the N-terminal glycine residue of cellular and viral proteins with diverse functions. N-myristoyltransferase (NMT; EC 2.3.1.97) catalyzes the transfer of myristate from CoA to proteins. N-myristoylation appears to be irreversible and is required for full expression of the biologic activities of several N-myristoylated proteins, including the alpha subunit of the signal-transducing guanine nucleotide-binding protein (G protein) GO (GNAO1; MIM 139311) (Duronio et al., 1992 [PubMed 1570339]).[supplied by OMIM, Nov 2008]

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.84).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.455 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
C1QL1NM_006688.5 linkc.598-1983A>T intron_variant Intron 1 of 1 ENST00000253407.4 NP_006679.1 O75973

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
C1QL1ENST00000253407.4 linkc.598-1983A>T intron_variant Intron 1 of 1 1 NM_006688.5 ENSP00000253407.2 O75973
NMT1ENST00000678938.1 linkc.-110+4288T>A intron_variant Intron 1 of 11 ENSP00000503621.1 P30419-2
C1QL1ENST00000718438.1 linkc.688-1983A>T intron_variant Intron 1 of 1 ENSP00000520823.1

Frequencies

GnomAD3 genomes
AF:
0.314
AC:
47716
AN:
151972
Hom.:
8247
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.449
Gnomad AMI
AF:
0.164
Gnomad AMR
AF:
0.273
Gnomad ASJ
AF:
0.248
Gnomad EAS
AF:
0.470
Gnomad SAS
AF:
0.260
Gnomad FIN
AF:
0.325
Gnomad MID
AF:
0.358
Gnomad NFE
AF:
0.237
Gnomad OTH
AF:
0.309
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.314
AC:
47777
AN:
152090
Hom.:
8264
Cov.:
32
AF XY:
0.318
AC XY:
23607
AN XY:
74342
show subpopulations
African (AFR)
AF:
0.449
AC:
18615
AN:
41468
American (AMR)
AF:
0.274
AC:
4184
AN:
15276
Ashkenazi Jewish (ASJ)
AF:
0.248
AC:
862
AN:
3472
East Asian (EAS)
AF:
0.471
AC:
2431
AN:
5166
South Asian (SAS)
AF:
0.259
AC:
1253
AN:
4830
European-Finnish (FIN)
AF:
0.325
AC:
3434
AN:
10580
Middle Eastern (MID)
AF:
0.354
AC:
104
AN:
294
European-Non Finnish (NFE)
AF:
0.237
AC:
16094
AN:
67984
Other (OTH)
AF:
0.309
AC:
651
AN:
2110
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.503
Heterozygous variant carriers
0
1622
3244
4865
6487
8109
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
468
936
1404
1872
2340
<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:
0.278
Hom.:
855
Bravo
AF:
0.319
Asia WGS
AF:
0.346
AC:
1201
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.84
CADD
Benign
4.7
DANN
Benign
0.81
PhyloP100
-0.024
Mutation Taster
=100/0
polymorphism (auto)

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

Other links and lift over

dbSNP: rs3024293; hg19: chr17-43039718; API