chr5-35934055-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

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

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.560
Variant links:
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]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
CAPSLNM_001042625.2 linkuse as main transcriptc.-1+4486A>G intron_variant ENST00000651391.1
CAPSLNM_144647.4 linkuse as main transcriptc.-1+4598A>G intron_variant
CAPSLXM_006714444.4 linkuse as main transcriptc.51+4499A>G intron_variant
CAPSLXM_006714445.4 linkuse as main transcriptc.51+4499A>G intron_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
CAPSLENST00000651391.1 linkuse as main transcriptc.-1+4486A>G intron_variant NM_001042625.2 P1

Frequencies

GnomAD3 genomes
AF:
0.226
AC:
34423
AN:
152062
Hom.:
4258
Cov.:
32
show subpopulations
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
show subpopulations
Gnomad4 AFR
AF:
0.122
Gnomad4 AMR
AF:
0.214
Gnomad4 ASJ
AF:
0.275
Gnomad4 EAS
AF:
0.162
Gnomad4 SAS
AF:
0.210
Gnomad4 FIN
AF:
0.345
Gnomad4 NFE
AF:
0.276
Gnomad4 OTH
AF:
0.219
Alfa
AF:
0.248
Hom.:
624
Bravo
AF:
0.213
Asia WGS
AF:
0.222
AC:
774
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.92
CADD
Benign
11
DANN
Benign
0.44

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

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs700172; hg19: chr5-35934157; API