7-88220357-CTTTT-CTT

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 0 publications found

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

ACMG classification

Our verdict: Benign. The variant received -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 VariationId 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.

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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SRI	NM_198901.2		c.7-1417_7-1416delAA		intron	N/A	NP_944490.1	P30626-2
	SRI	NM_001256892.2		c.7-1417_7-1416delAA		intron	N/A	NP_001243821.1	P30626-3
	SRI-AS1	NR_120517.1		n.574+1147_574+1148delTT		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SRI	ENST00000394641.7	TSL:2	c.7-1417_7-1416delAA		intron	N/A	ENSP00000378137.3	P30626-2
	SRI	ENST00000431660.5	TSL:2	c.7-1417_7-1416delAA		intron	N/A	ENSP00000391148.1	P30626-3
	SRI	ENST00000490437.5	TSL:2	c.7-3168_7-3167delAA		intron	N/A	ENSP00000418512.1	C9J0K6

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

African (AFR) AF: 0.747 AC: 30021 AN: 40202

American (AMR) AF: 0.670 AC: 9920 AN: 14810

Ashkenazi Jewish (ASJ) AF: 0.773 AC: 2659 AN: 3440

East Asian (EAS) AF: 0.256 AC: 1265 AN: 4946

South Asian (SAS) AF: 0.577 AC: 2680 AN: 4642

European-Finnish (FIN) AF: 0.775 AC: 7072 AN: 9124

Middle Eastern (MID) AF: 0.840 AC: 237 AN: 282

European-Non Finnish (NFE) AF: 0.810 AC: 54225 AN: 66948

Other (OTH) AF: 0.759 AC: 1552 AN: 2044

Alfa AF: 0.656 Hom.: 1242

ClinVar

ClinVar submissions

Significance: Benign

Revision: criteria provided, single submitter

Pathogenic	VUS	Benign	Condition
-	-	1	not provided (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		0.24
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs60686940; hg19: chr7-87849672;