1-151838436-C-G

Variant names:

• chr1-151838436-C-G
• rs1318643119
• NM_001394591.1:c.554G>C

Variant summary

Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2 BP4

The NM_001394591.1(C2CD4D):​c.554G>C​(p.Arg185Pro) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000237 in 1,267,194 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R185H) has been classified as Uncertain significance.

• Frequency:
  • Genomes: not found (cov: 33)
  • Exomes 𝑓: 0.0000024 (0 hom.)
• Consequence: C2CD4D NM_001394591.1 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.84

Genes affected

C2CD4D (HGNC:37210): (C2 calcium dependent domain containing 4D)

C2CD4D-AS1 (HGNC:54045): (C2CD4D and THEM5 antisense RNA 1)

ACMG classification

Verdict is Uncertain_significance. Variant got 1 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.41977707).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
C2CD4D	NM_001394591.1	c.554G>C	p.Arg185Pro	missense_variant	Exon 2 of 2	ENST00000694868.1	NP_001381520.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
C2CD4D	ENST00000694868.1	c.554G>C	p.Arg185Pro	missense_variant	Exon 2 of 2		NM_001394591.1	ENSP00000511551.1
C2CD4D	ENST00000454109.1	c.554G>C	p.Arg185Pro	missense_variant	Exon 2 of 2	2		ENSP00000389554.1
C2CD4D	ENST00000694869.1	c.554G>C	p.Arg185Pro	missense_variant	Exon 2 of 2			ENSP00000511552.1

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome AF: 0.00000237 AC: 3 AN: 1267194 Hom.: 0 Cov.: 32 AF XY: 0.00000321 AC XY: 2 AN XY: 622674

Gnomad4 AFR exome AF: 0.0000395

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 9.79e-7

Gnomad4 OTH exome AF: 0.0000192

GnomAD4 genome Cov.: 33

Bravo AF: 0.00000378

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.089
BayesDel_addAF	Benign	-0.11	T
BayesDel_noAF	Benign	-0.40
CADD	Benign	19
DANN	Uncertain	0.99
DEOGEN2	Benign	0.35	T
Eigen	Benign	0.14
Eigen_PC	Benign	-0.035
FATHMM_MKL	Benign	0.57	D
LIST_S2	Benign	0.50	T
M_CAP	Benign	0.061	D
MetaRNN	Benign	0.42	T
MetaSVM	Benign	-1.1	T
MutationAssessor	Uncertain	2.2	M
PrimateAI	Pathogenic	0.82	D
PROVEAN	Uncertain	-3.6	D
REVEL	Benign	0.098
Sift	Uncertain	0.019	D
Sift4G	Uncertain	0.0070	D
Polyphen		1.0	D
Vest4		0.25
MutPred		0.24		Gain of glycosylation at R185 (P = 0.0206);
MVP		0.40
ClinPred		0.99	D
GERP RS		1.9
Varity_R		0.46
gMVP		0.30

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: rs1318643119; hg19: chr1-151810912;