ENST00000613488.3:n.515C>T

Variant names:

• chr21-6116503-C-T
• rs1555841977
• ENST00000613488.3:n.515C>T

Variant summary

Our verdict is Uncertain significance. The variant received 2 ACMG points: 2P and 0B. PP3 PP5

The ENST00000613488.3(ENSG00000275993):​n.515C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Pathogenic (no stars).

• Frequency: Genomes: not found (cov: 0)
• Consequence: ENSG00000275993 ENST00000613488.3 non_coding_transcript_exon
• Clinical Significance: Pathogenic no assertion criteria provided P:1
• Conservation: PhyloP100: 1.20
• Publications: 0 publications found

Genes affected

ENSG00000275993 (HGNC:):

ACMG classification

Our verdict: Uncertain_significance. The variant received 2 ACMG points.

• PP3: MetaRNN computational evidence supports a deleterious effect, 0.808
• PP5: Variant 21-6116503-C-T is Pathogenic according to our data. Variant chr21-6116503-C-T is described in ClinVar as Pathogenic. ClinVar VariationId is 433140.Status of the report is no_assertion_criteria_provided, 0 stars.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000613488.3. 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
	LOC102724428	NM_001320643.3		c.379C>T	p.Arg127Trp	missense	Exon 5 of 14	NP_001307572.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000275993	ENST00000613488.3	TSL:1	n.515C>T		non_coding_transcript_exon	Exon 5 of 14

Frequencies

GnomAD3 genomes Cov.: 0

GnomAD4 exome Cov.: 0

GnomAD4 genome Cov.: 0

ClinVar

ClinVar submissions

Significance: Pathogenic

Revision: no assertion criteria provided

Pathogenic	VUS	Benign	Condition
1	-	-	Self-limited epilepsy with centrotemporal spikes (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Pathogenic	0.91
BayesDel_noAF	Benign	-0.78
CADD	Benign	12
LIST_S2	Pathogenic	0.99	D
MetaRNN	Pathogenic	0.81	D
PhyloP100		1.2
Sift4G	Pathogenic	0.0	D
gMVP		0.77

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: rs1555841977;

hg19: chr21-44841638;