rs1063964
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_003130.4(SRI):c.*324C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.295 in 359,442 control chromosomes in the GnomAD database, including 18,099 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 0.33 ( 9305 hom., cov: 32)
Exomes 𝑓: 0.27 ( 8794 hom. )
Consequence
SRI
NM_003130.4 3_prime_UTR
NM_003130.4 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.350
Genes affected
SRI (HGNC:11292): (sorcin) This gene encodes a calcium-binding protein with multiple E-F hand domains that relocates from the cytoplasm to the sarcoplasmic reticulum in response to elevated calcium levels. In addition to regulating intracellular calcium homeostasis it also modulates excitation-contraction coupling in the heart. Alternative splicing results in multiple transcript variants encoding distinct proteins. Multiple pseudogenes exist for this gene. [provided by RefSeq, Mar 2012]
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.88).
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.461 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SRI | NM_003130.4 | c.*324C>T | 3_prime_UTR_variant | 8/8 | ENST00000265729.7 | ||
SRI | NM_198901.2 | c.*324C>T | 3_prime_UTR_variant | 8/8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SRI | ENST00000265729.7 | c.*324C>T | 3_prime_UTR_variant | 8/8 | 1 | NM_003130.4 | P1 | ||
SRI | ENST00000419179.5 | c.*324C>T | 3_prime_UTR_variant | 8/8 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.333 AC: 50474AN: 151774Hom.: 9296 Cov.: 32
GnomAD3 genomes
?
AF:
AC:
50474
AN:
151774
Hom.:
Cov.:
32
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD4 exome AF: 0.267 AC: 55490AN: 207550Hom.: 8794 Cov.: 0 AF XY: 0.251 AC XY: 27834AN XY: 110692
GnomAD4 exome
AF:
AC:
55490
AN:
207550
Hom.:
Cov.:
0
AF XY:
AC XY:
27834
AN XY:
110692
Gnomad4 AFR exome
AF:
Gnomad4 AMR exome
AF:
Gnomad4 ASJ exome
AF:
Gnomad4 EAS exome
AF:
Gnomad4 SAS exome
AF:
Gnomad4 FIN exome
AF:
Gnomad4 NFE exome
AF:
Gnomad4 OTH exome
AF:
GnomAD4 genome ? AF: 0.333 AC: 50517AN: 151892Hom.: 9305 Cov.: 32 AF XY: 0.326 AC XY: 24179AN XY: 74238
GnomAD4 genome
?
AF:
AC:
50517
AN:
151892
Hom.:
Cov.:
32
AF XY:
AC XY:
24179
AN XY:
74238
Gnomad4 AFR
AF:
Gnomad4 AMR
AF:
Gnomad4 ASJ
AF:
Gnomad4 EAS
AF:
Gnomad4 SAS
AF:
Gnomad4 FIN
AF:
Gnomad4 NFE
AF:
Gnomad4 OTH
AF:
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
344
AN:
3476
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at