chr19-3623926-C-T

Position:

• chr19-3623926-C-T

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2 BP4_Moderate

The NM_001080543.2(CACTIN):​c.404G>A​(p.Ser135Asn) variant causes a missense 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. 13/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

• Frequency: Genomes: not found (cov: 33)
• Consequence: CACTIN NM_001080543.2 missense
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: 2.14

Genes affected

CACTIN (HGNC:29938): (cactin, spliceosome C complex subunit) Enables RNA binding activity. Involved in several processes, including cellular response to cytokine stimulus; negative regulation of cytokine production; and negative regulation of signal transduction. Located in cytosol and nuclear speck. Part of catalytic step 2 spliceosome. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Uncertain_significance. Variant got 0 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.11659959).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CACTIN	NM_001080543.2	c.404G>A	p.Ser135Asn	missense_variant	2/10	ENST00000429344.7	NP_001074012.1
CACTIN	NM_021231.2	c.404G>A	p.Ser135Asn	missense_variant	2/11		NP_067054.1
CACTIN	XM_011528160.3	c.404G>A	p.Ser135Asn	missense_variant	2/8		XP_011526462.1
CACTIN	XM_011528161.3	c.404G>A	p.Ser135Asn	missense_variant	2/7		XP_011526463.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CACTIN	ENST00000429344.7	c.404G>A	p.Ser135Asn	missense_variant	2/10	1	NM_001080543.2	ENSP00000415078	P1
CACTIN	ENST00000221899.7	c.404G>A	p.Ser135Asn	missense_variant	2/12	1		ENSP00000221899	P1
CACTIN	ENST00000585942.5	c.404G>A	p.Ser135Asn	missense_variant, NMD_transcript_variant	2/12	1		ENSP00000465751
CACTIN	ENST00000248420.9	c.404G>A	p.Ser135Asn	missense_variant	2/11	5		ENSP00000248420	P1

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Cov.: 31

GnomAD4 genome Cov.: 33

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: criteria provided, single submitter

Submissions by phenotype

not specified Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

Ambry Genetics

Aug 15, 2023

The c.404G>A (p.S135N) alteration is located in exon 2 (coding exon 2) of the CACTIN gene. This alteration results from a G to A substitution at nucleotide position 404, causing the serine (S) at amino acid position 135 to be replaced by an asparagine (N). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.12
BayesDel_addAF	Benign	-0.24	T
BayesDel_noAF	Benign	-0.58
CADD	Benign	22
DANN	Benign	0.97
DEOGEN2	Benign	0.012	T;T;T
Eigen	Benign	-0.23
Eigen_PC	Benign	-0.11
FATHMM_MKL	Benign	0.57	D
LIST_S2	Benign	0.64	.;.;T
M_CAP	Benign	0.017	T
MetaRNN	Benign	0.12	T;T;T
MetaSVM	Benign	-1.1	T
MutationAssessor	Uncertain	2.0	M;M;M
MutationTaster	Benign	0.99	N;N;N
PrimateAI	Uncertain	0.57	T
PROVEAN	Benign	-0.27	N;N;.
REVEL	Benign	0.049
Sift	Benign	0.40	T;T;.
Sift4G	Benign	0.49	T;T;T
Polyphen		0.047	B;B;B
Vest4		0.23
MutPred		0.26		Loss of phosphorylation at S135 (P = 0.0158);Loss of phosphorylation at S135 (P = 0.0158);Loss of phosphorylation at S135 (P = 0.0158);
MVP		0.16
MPC		0.58
ClinPred		0.18	T
GERP RS		3.5
Varity_R		0.091
gMVP		0.33

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

No publications associated with this variant yet.

Other links and lift over

hg19: chr19-3623924;