chr13-40941053-T-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 0P and 2B. BP4_Moderate
The NM_172373.4(ELF1):c.1124A>T(p.Gln375Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000137 in 1,461,886 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.1124A>T | p.Gln375Leu | missense_variant | 8/9 | ENST00000239882.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ELF1 | ENST00000239882.7 | c.1124A>T | p.Gln375Leu | missense_variant | 8/9 | 1 | NM_172373.4 | P1 | |
ELF1 | ENST00000635415.1 | c.1124A>T | p.Gln375Leu | missense_variant | 8/9 | 5 | |||
ELF1 | ENST00000625359.1 | c.1052A>T | p.Gln351Leu | missense_variant | 7/8 | 2 | |||
ELF1 | ENST00000498824.4 | c.*867A>T | 3_prime_UTR_variant, NMD_transcript_variant | 8/9 | 2 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD3 exomes AF: 0.00000398 AC: 1AN: 251490Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135922
GnomAD4 exome AF: 0.0000137 AC: 20AN: 1461886Hom.: 0 Cov.: 29 AF XY: 0.0000110 AC XY: 8AN XY: 727244
GnomAD4 genome ? Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Nov 21, 2023 | The c.1124A>T (p.Q375L) alteration is located in exon 8 (coding exon 7) of the ELF1 gene. This alteration results from a A to T substitution at nucleotide position 1124, causing the glutamine (Q) at amino acid position 375 to be replaced by a leucine (L). 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