rs1010601

Variant names:

• chr5-35908102-T-C
• rs1010601
• NM_001042625.2:c.525+1764A>G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 6 publications found

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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
CAPSL	NM_001042625.2	c.525+1764A>G		intron_variant	Intron 4 of 4	ENST00000651391.1	NP_001036090.1
CAPSL	NM_144647.4	c.525+1764A>G		intron_variant	Intron 4 of 4		NP_653248.3
CAPSL	XM_006714444.4	c.576+1764A>G		intron_variant	Intron 4 of 4		XP_006714507.1
CAPSL	XM_006714445.4	c.576+1764A>G		intron_variant	Intron 4 of 4		XP_006714508.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CAPSL	ENST00000651391.1	c.525+1764A>G		intron_variant	Intron 4 of 4		NM_001042625.2	ENSP00000498465.1
CAPSL	ENST00000397367.6	c.525+1764A>G		intron_variant	Intron 4 of 4	1		ENSP00000380524.2
CAPSL	ENST00000397366.5	c.525+1764A>G		intron_variant	Intron 4 of 4	3		ENSP00000380523.1
CAPSL	ENST00000513623.5	c.525+1764A>G		intron_variant	Intron 4 of 4	3		ENSP00000424806.1

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

African (AFR) AF: 0.540 AC: 22394 AN: 41476

American (AMR) AF: 0.326 AC: 4989 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.436 AC: 1511 AN: 3468

East Asian (EAS) AF: 0.0945 AC: 489 AN: 5174

South Asian (SAS) AF: 0.273 AC: 1314 AN: 4820

European-Finnish (FIN) AF: 0.411 AC: 4344 AN: 10578

Middle Eastern (MID) AF: 0.397 AC: 116 AN: 292

European-Non Finnish (NFE) AF: 0.432 AC: 29378 AN: 67988

Other (OTH) AF: 0.416 AC: 876 AN: 2108

Alfa AF: 0.440 Hom.: 1977

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
PhyloP100		-1.1
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs1010601; hg19: chr5-35908204;