6-4119187-T-G
Variant summary
Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PM2PP3_Moderate
The NM_206836.3(ECI2):āc.884A>Cā(p.Lys295Thr) variant causes a missense, splice region change. The variant allele was found at a frequency of 0.00000248 in 1,610,848 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. 2/3 splice prediction tools predicting alterations to normal splicing. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_206836.3 missense, splice_region
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ECI2 | NM_206836.3 | c.884A>C | p.Lys295Thr | missense_variant, splice_region_variant | 8/10 | ENST00000380118.8 | NP_996667.2 | |
TEX56P | NR_104463.3 | n.1307-2762T>G | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ECI2 | ENST00000380118.8 | c.884A>C | p.Lys295Thr | missense_variant, splice_region_variant | 8/10 | 1 | NM_206836.3 | ENSP00000369461 | P1 | |
TEX56P | ENST00000642280.1 | n.616-2762T>G | intron_variant, non_coding_transcript_variant | |||||||
TEX56P | ENST00000643110.1 | n.1050-2762T>G | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152214Hom.: 0 Cov.: 33
GnomAD4 exome AF: 0.00000206 AC: 3AN: 1458634Hom.: 0 Cov.: 31 AF XY: 0.00000276 AC XY: 2AN XY: 725646
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152214Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 74376
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 24, 2023 | The c.884A>C (p.K295T) alteration is located in exon 8 (coding exon 8) of the ECI2 gene. This alteration results from a A to C substitution at nucleotide position 884, causing the lysine (K) at amino acid position 295 to be replaced by a threonine (T). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at