rs75825892

Variant names:

• chr16-4207312-C-A
• rs75825892
• ENST00000572111.1:n.854G>T

Your query was ambiguous. Multiple possible variants found:

• chr16-4207312-C-A
• chr16-4207312-C-G
• chr16-4207312-C-T

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 2P and 2B. PM2 BP4_Moderate

The ENST00000572111.1(SRL):​n.854G>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: not found (cov: 33)
• Consequence: SRL ENST00000572111.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.986
• Publications: 4 publications found

Genes affected

SRL (HGNC:11295): (sarcalumenin) Predicted to enable GTP binding activity. Predicted to be involved in endocytosis and endosomal transport. Predicted to act upstream of or within response to muscle activity involved in regulation of muscle adaptation and store-operated calcium entry. Predicted to be located in sarcoplasmic reticulum lumen and sarcoplasmic reticulum membrane. Predicted to be active in intracellular membrane-bounded organelle. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (REVEL=0.035).

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000572111.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SRL	NM_001098814.2	MANE Select	c.62-2678G>T		intron	N/A	NP_001092284.1
	SRL	NM_001435440.1		c.854G>T	p.Ser285Ile	missense	Exon 2 of 7	NP_001422369.1
	SRL	NM_001323668.1		c.-651G>T		5_prime_UTR	Exon 2 of 7	NP_001310597.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SRL	ENST00000572111.1	TSL:1	n.854G>T		non_coding_transcript_exon	Exon 2 of 7	ENSP00000461179.1
	SRL	ENST00000399609.7	TSL:1 MANE Select	c.62-2678G>T		intron	N/A	ENSP00000382518.3
	SRL	ENST00000537996.1	TSL:2	c.-65-2678G>T		intron	N/A	ENSP00000440350.1

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Cov.: 0

GnomAD4 genome Cov.: 33

Alfa AF: 0.00 Hom.: 71

Bravo AF: 0.00000378

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.13
BayesDel_noAF	Benign	-0.81
CADD	Benign	2.5
DANN	Uncertain	0.99
PhyloP100		-0.99

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs75825892; hg19: chr16-4257313;