rs3024293

Variant names:

• chr17-44962350-T-A
• rs3024293
• NM_006688.5:c.598-1983A>T

Your query was ambiguous. Multiple possible variants found:

• chr17-44962350-T-A
• chr17-44962350-T-G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0240
• Publications: 2 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 -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
C1QL1	NM_006688.5	c.598-1983A>T		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.598-1983A>T		intron_variant	Intron 1 of 1	1	NM_006688.5	ENSP00000253407.2
NMT1	ENST00000678938.1	c.-110+4288T>A		intron_variant	Intron 1 of 11			ENSP00000503621.1
C1QL1	ENST00000718438.1	c.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

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

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

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

Other links and lift over

dbSNP: rs3024293; hg19: chr17-43039718;