13-40933447-A-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_172373.4(ELF1):c.1838T>A(p.Leu613Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000031 in 1,613,200 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_172373.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ELF1 | NM_172373.4 | c.1838T>A | p.Leu613Gln | missense_variant | 9/9 | ENST00000239882.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ELF1 | ENST00000239882.7 | c.1838T>A | p.Leu613Gln | missense_variant | 9/9 | 1 | NM_172373.4 | P1 | |
ELF1 | ENST00000635415.1 | c.1838T>A | p.Leu613Gln | missense_variant | 9/9 | 5 | |||
ELF1 | ENST00000625359.1 | c.1766T>A | p.Leu589Gln | missense_variant | 8/8 | 2 | |||
ELF1 | ENST00000498824.4 | c.*1581T>A | 3_prime_UTR_variant, NMD_transcript_variant | 9/9 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.00000657 AC: 1AN: 152232Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.00000398 AC: 1AN: 250952Hom.: 0 AF XY: 0.00000737 AC XY: 1AN XY: 135608
GnomAD4 exome AF: 0.00000274 AC: 4AN: 1460968Hom.: 0 Cov.: 30 AF XY: 0.00000275 AC XY: 2AN XY: 726678
GnomAD4 genome ? AF: 0.00000657 AC: 1AN: 152232Hom.: 0 Cov.: 33 AF XY: 0.0000134 AC XY: 1AN XY: 74370
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | May 03, 2023 | The c.1838T>A (p.L613Q) alteration is located in exon 9 (coding exon 8) of the ELF1 gene. This alteration results from a T to A substitution at nucleotide position 1838, causing the leucine (L) at amino acid position 613 to be replaced by a glutamine (Q). 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