Genetic Variant C1QL1:c.597+2628G>A (chr17-44964824-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The NM_006688.5(C1QL1):c.597+2628G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.629 in 151,872 control chromosomes in the GnomAD database, including 31,910 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 0.63 ( 31910 hom., cov: 31)

Consequence

C1QL1
NM_006688.5 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.103

Publications

1 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]

C1QL1 links:

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]

NMT1 links:

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=-0.92).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.867 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
C1QL1	NM_006688.5 link	c.597+2628G>A		intron_variant	Intron 1 of 1	ENST00000253407.4	NP_006679.1	O75973

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein	UniProt
C1QL1	ENST00000253407.4 link	c.597+2628G>A	intron_variant	Intron 1 of 1	1	NM_006688.5	ENSP00000253407.2	O75973
NMT1	ENST00000678938.1 link	c.-110+6762C>T	intron_variant	Intron 1 of 11			ENSP00000503621.1	P30419-2
C1QL1	ENST00000718438.1 link	c.687+2628G>A	intron_variant	Intron 1 of 1			ENSP00000520823.1

Frequencies

GnomAD3 genomes

AF:

0.628

AC:

95368

AN:

151752

Hom.:

31853

Cov.:

show subpopulations

Gnomad AFR

AF:

0.875

Gnomad AMI

AF:

0.389

Gnomad AMR

AF:

0.504

Gnomad ASJ

AF:

0.517

Gnomad EAS

AF:

0.510

Gnomad SAS

AF:

0.564

Gnomad FIN

AF:

0.524

Gnomad MID

AF:

0.599

Gnomad NFE

AF:

0.546

Gnomad OTH

AF:

0.593

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome

AF:

0.629

AC:

95476

AN:

151872

Hom.:

31910

Cov.:

AF XY:

0.622

AC XY:

46179

AN XY:

74194

show subpopulations

African (AFR)

AF:

0.875

AC:

36273

AN:

41466

American (AMR)

AF:

0.505

AC:

7703

AN:

15260

Ashkenazi Jewish (ASJ)

AF:

0.517

AC:

1795

AN:

3470

East Asian (EAS)

AF:

0.510

AC:

2632

AN:

5158

South Asian (SAS)

AF:

0.563

AC:

2714

AN:

4820

European-Finnish (FIN)

AF:

0.524

AC:

5491

AN:

10482

Middle Eastern (MID)

AF:

0.606

AC:

177

AN:

292

European-Non Finnish (NFE)

AF:

0.546

AC:

37101

AN:

67912

Other (OTH)

AF:

0.588

AC:

1237

AN:

2104

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

1615

3231

4846

6462

8077

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

760

1520

2280

3040

3800

<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:

0.597

Hom.:

5920

Bravo

AF:

0.636

Asia WGS

AF:

0.539

AC:

1875

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

3.7

(source)

DANN

Benign

0.26

PhyloP100

-0.10

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over