1-22645605-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_172369.5(C1QC):c.181+1401C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.51 in 152,024 control chromosomes in the GnomAD database, including 22,486 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 0.51 (22486 hom., cov: 32)
• Consequence: C1QC NM_172369.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.855

Genes affected

C1QC (HGNC:1245): (complement C1q C chain) This gene encodes the C-chain polypeptide of serum complement subcomponent C1q, which associates with C1r and C1s to yield the first component of the serum complement system. C1q is composed of 18 polypeptide chains which include 6 A-chains, 6 B-chains, and 6 C-chains. Each chain contains an N-terminal collagen-like region and a C-terminal C1q globular domain. C1q deficiency is associated with lupus erythematosus and glomerulonephritis. [provided by RefSeq, Dec 2016]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.792 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
C1QC	NM_172369.5	c.181+1401C>T		intron_variant		ENST00000374640.9
C1QC	NM_001114101.3	c.181+1401C>T		intron_variant
C1QC	NM_001347619.2	c.181+1401C>T		intron_variant
C1QC	NM_001347620.2	c.-86-1622C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
C1QC	ENST00000374640.9	c.181+1401C>T		intron_variant		1	NM_172369.5	P1

Frequencies

GnomAD3 genomes AF: 0.509 AC: 77396 AN: 151906 Hom.: 22450 Cov.: 32

Gnomad AFR AF: 0.799

Gnomad AMI AF: 0.260

Gnomad AMR AF: 0.484

Gnomad ASJ AF: 0.341

Gnomad EAS AF: 0.580

Gnomad SAS AF: 0.438

Gnomad FIN AF: 0.364

Gnomad MID AF: 0.361

Gnomad NFE AF: 0.375

Gnomad OTH AF: 0.486

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

GnomAD4 genome AF: 0.510 AC: 77474 AN: 152024 Hom.: 22486 Cov.: 32 AF XY: 0.509 AC XY: 37841 AN XY: 74304

Gnomad4 AFR AF: 0.799

Gnomad4 AMR AF: 0.483

Gnomad4 ASJ AF: 0.341

Gnomad4 EAS AF: 0.580

Gnomad4 SAS AF: 0.437

Gnomad4 FIN AF: 0.364

Gnomad4 NFE AF: 0.375

Gnomad4 OTH AF: 0.487

Alfa AF: 0.341 Hom.: 1265

Bravo AF: 0.534

Asia WGS AF: 0.526 AC: 1828 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	2.8
Dann	Benign	0.49

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

Other links and lift over

dbSNP: rs294183; hg19: chr1-22972098;