rs2361403

Variant names:

• chr5-35905109-C-T
• rs2361403
• NM_001042625.2:c.526-463G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_144647.4(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_144647.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -4.18
• Publications: 4 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=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.455 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_144647.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CAPSL	NM_001042625.2	MANE Select	c.526-463G>A		intron	N/A	NP_001036090.1
	CAPSL	NM_144647.4		c.526-463G>A		intron	N/A	NP_653248.3

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CAPSL	ENST00000651391.1	MANE Select	c.526-463G>A		intron	N/A	ENSP00000498465.1
	CAPSL	ENST00000397367.6	TSL:1	c.526-463G>A		intron	N/A	ENSP00000380524.2
	CAPSL	ENST00000397366.5	TSL:3	c.526-463G>A		intron	N/A	ENSP00000380523.1

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

African (AFR) AF: 0.461 AC: 19076 AN: 41418

American (AMR) AF: 0.319 AC: 4870 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.436 AC: 1513 AN: 3468

East Asian (EAS) AF: 0.0939 AC: 486 AN: 5174

South Asian (SAS) AF: 0.270 AC: 1298 AN: 4816

European-Finnish (FIN) AF: 0.410 AC: 4325 AN: 10538

Middle Eastern (MID) AF: 0.390 AC: 114 AN: 292

European-Non Finnish (NFE) AF: 0.432 AC: 29350 AN: 67956

Other (OTH) AF: 0.399 AC: 843 AN: 2112

Alfa AF: 0.419 Hom.: 38025

Bravo AF: 0.406

Asia WGS AF: 0.192 AC: 668 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.12
DANN	Benign	0.73
PhyloP100		-4.2
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: rs2361403; hg19: chr5-35905211;