Genetic Variant SRI:c.7-1416delA (chr7-88220357-CT-C) – ACMG Classification: Benign (-8 pts)

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BA1

The NM_198901.2(SRI):c.7-1416delA variant causes a intron change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.047 ( 527 hom., cov: 0)

Consequence

SRI
NM_198901.2 intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.660

Publications

0 publications found

Variant links:

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]

SRI links:

SRI-AS1 (HGNC:40564): (SRI antisense RNA 1)

SRI-AS1 links:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -8 ACMG points.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.154 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_198901.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	HGVSc	Effect	Exon Rank	Protein	UniProt
SRI	NM_198901.2	c.7-1416delA	intron	N/A	NP_944490.1	P30626-2
SRI	NM_001256892.2	c.7-1416delA	intron	N/A	NP_001243821.1	P30626-3
SRI-AS1	NR_120517.1	n.574+1148delT	intron	N/A

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
SRI	ENST00000394641.7	TSL:2	c.7-1416delA	intron	N/A	ENSP00000378137.3	P30626-2
SRI	ENST00000431660.5	TSL:2	c.7-1416delA	intron	N/A	ENSP00000391148.1	P30626-3
SRI	ENST00000490437.5	TSL:2	c.7-3167delA	intron	N/A	ENSP00000418512.1	C9J0K6

Frequencies

GnomAD3 genomes

AF:

0.0469

AC:

6895

AN:

147090

Hom.:

524

Cov.:

show subpopulations

Gnomad AFR

AF:

0.157

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0220

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00101

Gnomad SAS

AF:

0.00214

Gnomad FIN

AF:

0.00309

Gnomad MID

AF:

0.00658

Gnomad NFE

AF:

0.00245

Gnomad OTH

AF:

0.0316

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome

AF:

0.0471

AC:

6930

AN:

147144

Hom.:

527

Cov.:

AF XY:

0.0461

AC XY:

3288

AN XY:

71394

show subpopulations

African (AFR)

AF:

0.158

AC:

6331

AN:

40178

American (AMR)

AF:

0.0220

AC:

325

AN:

14794

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

3434

East Asian (EAS)

AF:

0.00101

AC:

AN:

4948

South Asian (SAS)

AF:

0.00215

AC:

AN:

4652

European-Finnish (FIN)

AF:

0.00309

AC:

AN:

9060

Middle Eastern (MID)

AF:

0.00714

AC:

AN:

280

European-Non Finnish (NFE)

AF:

0.00245

AC:

164

AN:

66860

Other (OTH)

AF:

0.0319

AC:

AN:

2040

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.481

Heterozygous variant carriers

273

545

818

1090

1363

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

140

210

280

350

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.00220

Hom.:

1242

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

PhyloP100

-0.66

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

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7-88220357-CTTTT-CTTT

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over