7-88220357-CTT-C

Variant names:

• chr7-88220357-CTT-C
• rs60686940
• NM_198901.2:c.7-1417_7-1416delAA

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_Moderate BA1

The NM_198901.2(SRI):​c.7-1417_7-1416delAA variant causes a intron change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.75 (42080 hom., cov: 0)
• Consequence: SRI NM_198901.2 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.245

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]

ENSG00000228113 (HGNC:):

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

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP6: Variant 7-88220357-CTT-C is Benign according to our data. Variant chr7-88220357-CTT-C is described in ClinVar as [Benign]. Clinvar id is 1262145.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.804 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SRI	NM_198901.2	c.7-1417_7-1416delAA		intron_variant	Intron 1 of 7		NP_944490.1
SRI	NM_001256892.2	c.7-1417_7-1416delAA		intron_variant	Intron 1 of 6		NP_001243821.1
SRI-AS1	NR_120517.1	n.574+1147_574+1148delTT		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SRI	ENST00000394641.7	c.7-1417_7-1416delAA		intron_variant	Intron 1 of 7	2		ENSP00000378137.3
SRI	ENST00000431660.5	c.7-1417_7-1416delAA		intron_variant	Intron 1 of 6	2		ENSP00000391148.1
SRI	ENST00000490437.5	c.7-3168_7-3167delAA		intron_variant	Intron 1 of 6	2		ENSP00000418512.1

Frequencies

GnomAD3 genomes AF: 0.750 AC: 110400 AN: 147282 Hom.: 42079 Cov.: 0

Gnomad AFR AF: 0.747

Gnomad AMI AF: 0.881

Gnomad AMR AF: 0.670

Gnomad ASJ AF: 0.773

Gnomad EAS AF: 0.256

Gnomad SAS AF: 0.577

Gnomad FIN AF: 0.775

Gnomad MID AF: 0.846

Gnomad NFE AF: 0.810

Gnomad OTH AF: 0.761

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

GnomAD4 genome AF: 0.749 AC: 110422 AN: 147336 Hom.: 42080 Cov.: 0 AF XY: 0.741 AC XY: 52969 AN XY: 71516

Gnomad4 AFR AF: 0.747

Gnomad4 AMR AF: 0.670

Gnomad4 ASJ AF: 0.773

Gnomad4 EAS AF: 0.256

Gnomad4 SAS AF: 0.577

Gnomad4 FIN AF: 0.775

Gnomad4 NFE AF: 0.810

Gnomad4 OTH AF: 0.759

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Jun 19, 2021

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

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Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs60686940; hg19: chr7-87849672;