rs1445898

Positions:

• chr5-35910427-C-A
• chr5-35910427-C-T

Variant summary

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

The NM_001042625.2(CAPSL):​c.254G>T​(p.Arg85Leu) 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. 15/21 in silico tools predict 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. R85Q) has been classified as Likely benign.

• Frequency: Genomes: not found (cov: 32)
• Consequence: CAPSL NM_001042625.2 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.981

Genes affected

CAPSL (HGNC:28375): (calcyphosine like) Predicted to enable calcium ion binding activity. Predicted to be located in cytoplasm. [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=0.10772854).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CAPSL	NM_001042625.2	c.254G>T	p.Arg85Leu	missense_variant	3/5	ENST00000651391.1	NP_001036090.1
CAPSL	NM_144647.4	c.254G>T	p.Arg85Leu	missense_variant	3/5		NP_653248.3
CAPSL	XM_006714444.4	c.305G>T	p.Arg102Leu	missense_variant	3/5		XP_006714507.1
CAPSL	XM_006714445.4	c.305G>T	p.Arg102Leu	missense_variant	3/5		XP_006714508.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CAPSL	ENST00000651391.1	c.254G>T	p.Arg85Leu	missense_variant	3/5		NM_001042625.2	ENSP00000498465	P1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 37

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.13
BayesDel_addAF	Benign	-0.12	T
BayesDel_noAF	Benign	-0.41
CADD	Benign	12
DANN	Benign	0.94
DEOGEN2	Benign	0.39	T;T;.;.
Eigen	Benign	-1.0
Eigen_PC	Benign	-1.0
FATHMM_MKL	Benign	0.14	N
LIST_S2	Uncertain	0.88	.;D;D;D
M_CAP	Benign	0.062	D
MetaRNN	Benign	0.11	T;T;T;T
MetaSVM	Benign	-0.76	T
MutationAssessor	Benign	1.8	L;L;.;.
MutationTaster	Benign	1.0	P;P;P
PrimateAI	Benign	0.24	T
PROVEAN	Uncertain	-2.6	D;D;D;D
REVEL	Benign	0.12
Sift	Benign	0.10	T;T;T;T
Sift4G	Benign	0.30	T;T;T;T
Polyphen		0.0080	B;B;.;.
Vest4		0.52
MutPred		0.49		Loss of disorder (P = 0.05);Loss of disorder (P = 0.05);Loss of disorder (P = 0.05);Loss of disorder (P = 0.05);
MVP		0.40
MPC		0.020
ClinPred		0.066	T
GERP RS		0.53
Varity_R		0.13
gMVP		0.67

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: rs1445898; hg19: chr5-35910529;