rs3024275

Variant names:

• chr17-44965985-G-C
• rs3024275
• NM_006688.5:c.597+1467C>G

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The NM_006688.5(C1QL1):​c.597+1467C>G variant causes a intron change. The variant allele was found at a frequency of 0.143 in 152,214 control chromosomes in the GnomAD database, including 1,655 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 0.14 (1655 hom., cov: 32)
• Consequence: C1QL1 NM_006688.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.60
• Publications: 1 publications found

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]

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.33).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.243 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
C1QL1	NM_006688.5	c.597+1467C>G		intron_variant	Intron 1 of 1	ENST00000253407.4	NP_006679.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
C1QL1	ENST00000253407.4	c.597+1467C>G		intron_variant	Intron 1 of 1	1	NM_006688.5	ENSP00000253407.2
NMT1	ENST00000678938.1	c.-110+7923G>C		intron_variant	Intron 1 of 11			ENSP00000503621.1
C1QL1	ENST00000718438.1	c.687+1467C>G		intron_variant	Intron 1 of 1			ENSP00000520823.1

Frequencies

GnomAD3 genomes AF: 0.143 AC: 21713 AN: 152096 Hom.: 1652 Cov.: 32

Gnomad AFR AF: 0.152

Gnomad AMI AF: 0.137

Gnomad AMR AF: 0.157

Gnomad ASJ AF: 0.101

Gnomad EAS AF: 0.254

Gnomad SAS AF: 0.107

Gnomad FIN AF: 0.182

Gnomad MID AF: 0.139

Gnomad NFE AF: 0.124

Gnomad OTH AF: 0.144

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

GnomAD4 genome AF: 0.143 AC: 21736 AN: 152214 Hom.: 1655 Cov.: 32 AF XY: 0.145 AC XY: 10793 AN XY: 74406

African (AFR) AF: 0.152 AC: 6317 AN: 41542

American (AMR) AF: 0.157 AC: 2407 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.101 AC: 351 AN: 3466

East Asian (EAS) AF: 0.254 AC: 1317 AN: 5180

South Asian (SAS) AF: 0.107 AC: 518 AN: 4826

European-Finnish (FIN) AF: 0.182 AC: 1930 AN: 10588

Middle Eastern (MID) AF: 0.143 AC: 42 AN: 294

European-Non Finnish (NFE) AF: 0.124 AC: 8423 AN: 68012

Other (OTH) AF: 0.145 AC: 306 AN: 2112

Alfa AF: 0.141 Hom.: 179

Bravo AF: 0.144

Asia WGS AF: 0.151 AC: 522 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.33
CADD	Benign	17
DANN	Benign	0.57
PhyloP100		3.6
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

Other links and lift over

dbSNP: rs3024275; hg19: chr17-43043353; COSMIC: COSV53648140;