3-113623530-AAG-GAA

Variant names:

• chr3-113623530-AAG-GAA
• ENST00000264852.9:c.2183_2185delAAGinsGAA

Variant summary

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

The ENST00000264852.9(SIDT1):​c.2183_2185delAAGinsGAA​(p.Tyr728*) variant causes a stop gained change involving the alteration of a conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. It is difficult to determine the true allele frequency of this variant because it is of type MNV, and the frequency of such variant types in population databases may be underestimated and unreliable. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Variant results in nonsense mediated mRNA decay.

• Frequency: Genomes: not found (cov: 32)
• Consequence: SIDT1 ENST00000264852.9 stop_gained
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 9.60
• Publications: 0 publications found

Genes affected

SIDT1 (HGNC:25967): (SID1 transmembrane family member 1) The protein encoded by this gene belongs to SID1 family of transmembrane dsRNA-gated channels. Family members transport dsRNA into cells and are required for systemic RNA interference. [provided by RefSeq, May 2017]

LOC124909410 (HGNC:):

ACMG classification

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

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000264852.9. 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
	SIDT1	NM_017699.3	MANE Select	c.2194_2196delAAGinsGAA	p.Lys732Glu	missense splice_region	N/A	NP_060169.2	Q9NXL6-1
	SIDT1	NM_001322294.2		c.2212_2214delAAGinsGAA	p.Lys738Glu	missense splice_region	N/A	NP_001309223.1
	SIDT1	NM_001308350.2		c.2209_2211delAAGinsGAA	p.Lys737Glu	missense splice_region	N/A	NP_001295279.1	Q9NXL6-2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SIDT1	ENST00000264852.9	TSL:2 MANE Select	c.2183_2185delAAGinsGAA	p.Tyr728*	stop_gained	N/A	ENSP00000264852.4	Q9NXL6-1
	SIDT1	ENST00000393830.5	TSL:1	c.2198_2200delAAGinsGAA	p.Tyr733*	stop_gained	N/A	ENSP00000377416.4	Q9NXL6-2
	SIDT1	ENST00000950250.1		c.2243_2245delAAGinsGAA	p.Tyr748*	stop_gained	N/A	ENSP00000620309.1

Frequencies

GnomAD3 genomes Cov.: 32

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

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		9.6

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

hg19: chr3-113342377;