6-138814569-G-A
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_StrongBS1_SupportingBS2
The NM_001077706.3(ECT2L):c.145G>A(p.Ala49Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00132 in 1,611,060 control chromosomes in the GnomAD database, including 32 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as not provided (no stars).
Frequency
Consequence
NM_001077706.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -9 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ECT2L | NM_001077706.3 | c.145G>A | p.Ala49Thr | missense_variant | 4/22 | ENST00000541398.7 | NP_001071174.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ECT2L | ENST00000541398.7 | c.145G>A | p.Ala49Thr | missense_variant | 4/22 | 5 | NM_001077706.3 | ENSP00000442307 | P1 | |
ECT2L | ENST00000367682.6 | c.145G>A | p.Ala49Thr | missense_variant | 3/21 | 5 | ENSP00000356655 | P1 | ||
ECT2L | ENST00000401414.4 | c.145G>A | p.Ala49Thr | missense_variant | 3/3 | 4 | ENSP00000385187 |
Frequencies
GnomAD3 genomes AF: 0.00727 AC: 1105AN: 151980Hom.: 17 Cov.: 32
GnomAD3 exomes AF: 0.00201 AC: 501AN: 248934Hom.: 9 AF XY: 0.00158 AC XY: 213AN XY: 135106
GnomAD4 exome AF: 0.000699 AC: 1020AN: 1458962Hom.: 15 Cov.: 30 AF XY: 0.000593 AC XY: 430AN XY: 725674
GnomAD4 genome AF: 0.00728 AC: 1108AN: 152098Hom.: 17 Cov.: 32 AF XY: 0.00720 AC XY: 535AN XY: 74354
ClinVar
Submissions by phenotype
not specified Other:1
not provided, no classification provided | reference population | ITMI | Sep 19, 2013 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at