chr5-96613298-T-C

Variant summary

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

The NR_130776.1(LOC101929710):​n.355-17669T>C variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.283 in 152,048 control chromosomes in the GnomAD database, including 7,582 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 0.28 ( 7582 hom., cov: 32)

Consequence

LOC101929710
NR_130776.1 intron, non_coding_transcript

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.250
Variant links:
Genes affected
CAST (HGNC:1515): (calpastatin) The protein encoded by this gene is an endogenous calpain (calcium-dependent cysteine protease) inhibitor. It consists of an N-terminal domain L and four repetitive calpain-inhibition domains (domains 1-4), and it is involved in the proteolysis of amyloid precursor protein. The calpain/calpastatin system is involved in numerous membrane fusion events, such as neural vesicle exocytosis and platelet and red-cell aggregation. The encoded protein is also thought to affect the expression levels of genes encoding structural or regulatory proteins. Alternatively spliced transcript variants encoding different isoforms have been described. [provided by RefSeq, Jun 2010]

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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=-0.93).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.49 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
LOC101929710NR_130776.1 linkuse as main transcriptn.355-17669T>C intron_variant, non_coding_transcript_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
ENST00000502645.2 linkuse as main transcriptn.355-17669T>C intron_variant, non_coding_transcript_variant 5
CASTENST00000505143.5 linkuse as main transcriptc.61-62241T>C intron_variant 3
ENST00000513158.1 linkuse as main transcriptn.542-17669T>C intron_variant, non_coding_transcript_variant 3

Frequencies

GnomAD3 genomes
AF:
0.283
AC:
42992
AN:
151930
Hom.:
7550
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.496
Gnomad AMI
AF:
0.150
Gnomad AMR
AF:
0.296
Gnomad ASJ
AF:
0.189
Gnomad EAS
AF:
0.353
Gnomad SAS
AF:
0.146
Gnomad FIN
AF:
0.222
Gnomad MID
AF:
0.161
Gnomad NFE
AF:
0.173
Gnomad OTH
AF:
0.238
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.283
AC:
43073
AN:
152048
Hom.:
7582
Cov.:
32
AF XY:
0.283
AC XY:
21060
AN XY:
74346
show subpopulations
Gnomad4 AFR
AF:
0.496
Gnomad4 AMR
AF:
0.296
Gnomad4 ASJ
AF:
0.189
Gnomad4 EAS
AF:
0.354
Gnomad4 SAS
AF:
0.146
Gnomad4 FIN
AF:
0.222
Gnomad4 NFE
AF:
0.173
Gnomad4 OTH
AF:
0.241
Alfa
AF:
0.189
Hom.:
6312
Bravo
AF:
0.300
Asia WGS
AF:
0.281
AC:
979
AN:
3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.93
CADD
Benign
1.9
DANN
Benign
0.64

Splicing

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: rs6885297; hg19: chr5-95949002; API