rs2361403

Positions:

• chr5-35905109-C-T

Variant summary

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

The NM_001042625.2(CAPSL):​c.526-463G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.41 in 151,954 control chromosomes in the GnomAD database, including 13,227 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 0.41 (13227 hom., cov: 31)
• Consequence: CAPSL NM_001042625.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -4.18

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=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.455 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CAPSL	NM_001042625.2	c.526-463G>A		intron_variant		ENST00000651391.1	NP_001036090.1
CAPSL	NM_144647.4	c.526-463G>A		intron_variant			NP_653248.3
CAPSL	XM_006714444.4	c.577-463G>A		intron_variant			XP_006714507.1
CAPSL	XM_006714445.4	c.577-390G>A		intron_variant			XP_006714508.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CAPSL	ENST00000651391.1	c.526-463G>A		intron_variant			NM_001042625.2	ENSP00000498465	P1
CAPSL	ENST00000397367.6	c.526-463G>A		intron_variant		1		ENSP00000380524	P1
CAPSL	ENST00000397366.5	c.526-463G>A		intron_variant		3		ENSP00000380523	P1
CAPSL	ENST00000513623.5	c.526-463G>A		intron_variant		3		ENSP00000424806

Frequencies

GnomAD3 genomes AF: 0.410 AC: 62306 AN: 151836 Hom.: 13222 Cov.: 31

Gnomad AFR AF: 0.461

Gnomad AMI AF: 0.493

Gnomad AMR AF: 0.319

Gnomad ASJ AF: 0.436

Gnomad EAS AF: 0.0935

Gnomad SAS AF: 0.270

Gnomad FIN AF: 0.410

Gnomad MID AF: 0.382

Gnomad NFE AF: 0.432

Gnomad OTH AF: 0.404

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

GnomAD4 genome AF: 0.410 AC: 62324 AN: 151954 Hom.: 13227 Cov.: 31 AF XY: 0.403 AC XY: 29901 AN XY: 74278

Gnomad4 AFR AF: 0.461

Gnomad4 AMR AF: 0.319

Gnomad4 ASJ AF: 0.436

Gnomad4 EAS AF: 0.0939

Gnomad4 SAS AF: 0.270

Gnomad4 FIN AF: 0.410

Gnomad4 NFE AF: 0.432

Gnomad4 OTH AF: 0.399

Alfa AF: 0.421 Hom.: 24033

Bravo AF: 0.406

Asia WGS AF: 0.192 AC: 668 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.12
DANN	Benign	0.73

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: rs2361403; hg19: chr5-35905211;