ENST00000594469.5:n.128+7714A>G

Variant names:

• chr7-88227200-A-G
• rs43111
• ENST00000594469.5:n.128+7714A>G

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The ENST00000594469.5(ENSG00000228113):​n.128+7714A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.564 in 151,980 control chromosomes in the GnomAD database, including 24,495 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.56 (24495 hom., cov: 31)
• Consequence: ENSG00000228113 ENST00000594469.5 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.892

Genes affected

ENSG00000228113 (HGNC:):

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

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]

ACMG classification

Verdict is Benign. Variant got -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BP6: Variant 7-88227200-A-G is Benign according to our data. Variant chr7-88227200-A-G is described in ClinVar as [Benign]. Clinvar id is 1281341.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.789 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SRI-AS1	NR_120517.1	n.575-2556A>G		intron_variant	Intron 2 of 2
SRI	NM_198901.2	c.-286T>C		upstream_gene_variant			NP_944490.1
SRI	NM_001256892.2	c.-286T>C		upstream_gene_variant			NP_001243821.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000228113	ENST00000594469.5	n.128+7714A>G		intron_variant	Intron 1 of 2	5
SRI	ENST00000394641.7	c.-286T>C		upstream_gene_variant		2		ENSP00000378137.3
SRI	ENST00000431660.5	c.-286T>C		upstream_gene_variant		2		ENSP00000391148.1

Frequencies

GnomAD3 genomes AF: 0.564 AC: 85606 AN: 151862 Hom.: 24477 Cov.: 31

Gnomad AFR AF: 0.477

Gnomad AMI AF: 0.624

Gnomad AMR AF: 0.622

Gnomad ASJ AF: 0.565

Gnomad EAS AF: 0.811

Gnomad SAS AF: 0.653

Gnomad FIN AF: 0.526

Gnomad MID AF: 0.497

Gnomad NFE AF: 0.583

Gnomad OTH AF: 0.565

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

GnomAD4 genome AF: 0.564 AC: 85670 AN: 151980 Hom.: 24495 Cov.: 31 AF XY: 0.563 AC XY: 41830 AN XY: 74276

Gnomad4 AFR AF: 0.477

Gnomad4 AMR AF: 0.621

Gnomad4 ASJ AF: 0.565

Gnomad4 EAS AF: 0.810

Gnomad4 SAS AF: 0.654

Gnomad4 FIN AF: 0.526

Gnomad4 NFE AF: 0.583

Gnomad4 OTH AF: 0.564

Alfa AF: 0.579 Hom.: 43799

Bravo AF: 0.568

Asia WGS AF: 0.697 AC: 2421 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

May 15, 2021

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

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Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	0.22
DANN	Benign	0.51

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs43111; hg19: chr7-87856515;