rs700172

chr5-35934055-T-C

Variant summary

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

The NM_001042625.2(CAPSL):c.-1+4486A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.226 in 152,180 control chromosomes in the GnomAD database, including 4,252 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 0.23 (4252 hom., cov: 32)
• Consequence: CAPSL NM_001042625.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.560

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 Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.273 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CAPSL	NM_001042625.2	c.-1+4486A>G		intron_variant		ENST00000651391.1
CAPSL	NM_144647.4	c.-1+4598A>G		intron_variant
CAPSL	XM_006714444.4	c.51+4499A>G		intron_variant
CAPSL	XM_006714445.4	c.51+4499A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CAPSL	ENST00000651391.1	c.-1+4486A>G		intron_variant			NM_001042625.2	P1

Frequencies

GnomAD3 genomes AF: 0.226 AC: 34423 AN: 152062 Hom.: 4258 Cov.: 32

Gnomad AFR AF: 0.122

Gnomad AMI AF: 0.368

Gnomad AMR AF: 0.214

Gnomad ASJ AF: 0.275

Gnomad EAS AF: 0.162

Gnomad SAS AF: 0.211

Gnomad FIN AF: 0.345

Gnomad MID AF: 0.269

Gnomad NFE AF: 0.276

Gnomad OTH AF: 0.217

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

GnomAD4 genome AF: 0.226 AC: 34423 AN: 152180 Hom.: 4252 Cov.: 32 AF XY: 0.228 AC XY: 16985 AN XY: 74414

Gnomad4 AFR AF: 0.122

Gnomad4 AMR AF: 0.214

Gnomad4 ASJ AF: 0.275

Gnomad4 EAS AF: 0.162

Gnomad4 SAS AF: 0.210

Gnomad4 FIN AF: 0.345

Gnomad4 NFE AF: 0.276

Gnomad4 OTH AF: 0.219

Alfa AF: 0.248 Hom.: 624

Bravo AF: 0.213

Asia WGS AF: 0.222 AC: 774 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	11
Dann	Benign	0.44

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: rs700172; hg19: chr5-35934157;