12-7096079-C-A

Variant names:

• chr12-7096079-C-A
• rs3782928
• NM_016546.4:c.*312G>T

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_016546.4(C1RL):​c.*312G>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 32)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: C1RL NM_016546.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.457
• Publications: 17 publications found

Genes affected

C1RL (HGNC:21265): (complement C1r subcomponent like) Predicted to enable serine-type endopeptidase activity. Predicted to be involved in zymogen activation. Located in extracellular exosome. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_016546.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	C1RL	NM_016546.4	MANE Select	c.*312G>T		3_prime_UTR	Exon 6 of 6	NP_057630.2	Q9NZP8
	C1RL	NM_001297640.2		c.*312G>T		3_prime_UTR	Exon 5 of 5	NP_001284569.1
	C1RL	NM_001297642.2		c.*878G>T		3_prime_UTR	Exon 6 of 6	NP_001284571.1	F5GWF3

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	C1RL	ENST00000266542.9	TSL:1 MANE Select	c.*312G>T		3_prime_UTR	Exon 6 of 6	ENSP00000266542.4	Q9NZP8
	C1RL	ENST00000872919.1		c.*312G>T		3_prime_UTR	Exon 6 of 6	ENSP00000542978.1
	C1RL	ENST00000872920.1		c.*312G>T		3_prime_UTR	Exon 6 of 6	ENSP00000542979.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 956274 Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0 AN XY: 447102

African (AFR) AF: 0.00 AC: 0 AN: 19852

American (AMR) AF: 0.00 AC: 0 AN: 5582

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 9786

East Asian (EAS) AF: 0.00 AC: 0 AN: 12140

South Asian (SAS) AF: 0.00 AC: 0 AN: 21958

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 7948

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 2290

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 841206

Other (OTH) AF: 0.00 AC: 0 AN: 35512

GnomAD4 genome Cov.: 32

Alfa AF: 0.00 Hom.: 24024

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	0.89
DANN	Benign	0.61
PhyloP100		-0.46

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: rs3782928; hg19: chr12-7248675;