rs1010601

Positions:

• chr5-35908102-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.525+1764A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.433 in 152,094 control chromosomes in the GnomAD database, including 14,958 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 0.43 (14958 hom., cov: 33)
• Consequence: CAPSL NM_001042625.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.06

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=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.534 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CAPSL	NM_001042625.2	c.525+1764A>G		intron_variant		ENST00000651391.1
CAPSL	NM_144647.4	c.525+1764A>G		intron_variant
CAPSL	XM_006714444.4	c.576+1764A>G		intron_variant
CAPSL	XM_006714445.4	c.576+1764A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CAPSL	ENST00000651391.1	c.525+1764A>G		intron_variant			NM_001042625.2	P1
CAPSL	ENST00000397367.6	c.525+1764A>G		intron_variant		1		P1
CAPSL	ENST00000397366.5	c.525+1764A>G		intron_variant		3		P1
CAPSL	ENST00000513623.5	c.525+1764A>G		intron_variant		3

Frequencies

GnomAD3 genomes AF: 0.433 AC: 65825 AN: 151978 Hom.: 14949 Cov.: 33

Gnomad AFR AF: 0.541

Gnomad AMI AF: 0.492

Gnomad AMR AF: 0.327

Gnomad ASJ AF: 0.436

Gnomad EAS AF: 0.0941

Gnomad SAS AF: 0.273

Gnomad FIN AF: 0.411

Gnomad MID AF: 0.396

Gnomad NFE AF: 0.432

Gnomad OTH AF: 0.420

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

GnomAD4 genome AF: 0.433 AC: 65858 AN: 152094 Hom.: 14958 Cov.: 33 AF XY: 0.425 AC XY: 31617 AN XY: 74336

Gnomad4 AFR AF: 0.540

Gnomad4 AMR AF: 0.326

Gnomad4 ASJ AF: 0.436

Gnomad4 EAS AF: 0.0945

Gnomad4 SAS AF: 0.273

Gnomad4 FIN AF: 0.411

Gnomad4 NFE AF: 0.432

Gnomad4 OTH AF: 0.416

Alfa AF: 0.436 Hom.: 1876

Bravo AF: 0.431

Asia WGS AF: 0.201 AC: 699 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.35
DANN	Benign	0.35

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: rs1010601; hg19: chr5-35908204;