7-88220357-CTTTT-CTTTTT

Variant names:

• chr7-88220357-C-CT
• rs60686940
• NM_198901.2:c.7-1416dupA

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BS2

The NM_198901.2(SRI):​c.7-1416dupA 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 0.00032 (1 hom., cov: 0)
• Consequence: SRI NM_198901.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.660
• 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: Likely_benign. The variant received -4 ACMG points.

• BS2: High AC in GnomAd4 at 47 AD gene.

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.7-1416dupA		intron	N/A	NP_944490.1	P30626-2
	SRI	NM_001256892.2		c.7-1416dupA		intron	N/A	NP_001243821.1	P30626-3
	SRI-AS1	NR_120517.1		n.574+1148dupT		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SRI	ENST00000394641.7	TSL:2	c.7-1416_7-1415insA		intron	N/A	ENSP00000378137.3	P30626-2
	SRI	ENST00000431660.5	TSL:2	c.7-1416_7-1415insA		intron	N/A	ENSP00000391148.1	P30626-3
	SRI	ENST00000490437.5	TSL:2	c.7-3167_7-3166insA		intron	N/A	ENSP00000418512.1	C9J0K6

Frequencies

GnomAD3 genomes AF: 0.000319 AC: 47 AN: 147344 Hom.: 1 Cov.: 0

Gnomad AFR AF: 0.0000249

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000338

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00444

Gnomad SAS AF: 0.00236

Gnomad FIN AF: 0.000219

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0000896

Gnomad OTH AF: 0.00

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

GnomAD4 genome AF: 0.000319 AC: 47 AN: 147398 Hom.: 1 Cov.: 0 AF XY: 0.000363 AC XY: 26 AN XY: 71544

African (AFR) AF: 0.0000249 AC: 1 AN: 40222

American (AMR) AF: 0.000337 AC: 5 AN: 14818

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3440

East Asian (EAS) AF: 0.00445 AC: 22 AN: 4942

South Asian (SAS) AF: 0.00237 AC: 11 AN: 4650

European-Finnish (FIN) AF: 0.000219 AC: 2 AN: 9128

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 282

European-Non Finnish (NFE) AF: 0.0000896 AC: 6 AN: 66972

Other (OTH) AF: 0.00 AC: 0 AN: 2046

Alfa AF: 0.00 Hom.: 1242

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		-0.66

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;