chr5-35934055-T-C

Variant names:

• chr5-35934055-T-C
• rs700172
• NM_001042625.2:c.-1+4486A>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.-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
• Publications: 5 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=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.273 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001042625.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CAPSL	NM_001042625.2	MANE Select	c.-1+4486A>G		intron	N/A	NP_001036090.1
	CAPSL	NM_144647.4		c.-1+4598A>G		intron	N/A	NP_653248.3

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CAPSL	ENST00000651391.1	MANE Select	c.-1+4486A>G		intron	N/A	ENSP00000498465.1
	CAPSL	ENST00000397367.6	TSL:1	c.-1+4598A>G		intron	N/A	ENSP00000380524.2
	CAPSL	ENST00000397366.5	TSL:3	c.-1+4486A>G		intron	N/A	ENSP00000380523.1

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

African (AFR) AF: 0.122 AC: 5057 AN: 41538

American (AMR) AF: 0.214 AC: 3271 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.275 AC: 954 AN: 3466

East Asian (EAS) AF: 0.162 AC: 839 AN: 5172

South Asian (SAS) AF: 0.210 AC: 1012 AN: 4810

European-Finnish (FIN) AF: 0.345 AC: 3649 AN: 10588

Middle Eastern (MID) AF: 0.265 AC: 78 AN: 294

European-Non Finnish (NFE) AF: 0.276 AC: 18766 AN: 67988

Other (OTH) AF: 0.219 AC: 463 AN: 2116

Alfa AF: 0.243 Hom.: 628

Bravo AF: 0.213

Asia WGS AF: 0.222 AC: 774 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	11
DANN	Benign	0.44
PhyloP100		0.56
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: rs700172; hg19: chr5-35934157;