chrX-47638007-G-A
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_001114123.3(ELK1):c.830C>T(p.Pro277Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000319 in 1,097,634 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 7 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001114123.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ELK1 | NM_001114123.3 | c.830C>T | p.Pro277Leu | missense_variant | 5/7 | ENST00000376983.8 | |
ELK1 | NM_005229.4 | c.830C>T | p.Pro277Leu | missense_variant | 4/6 | ||
ELK1 | NM_001257168.1 | c.271-955C>T | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ELK1 | ENST00000376983.8 | c.830C>T | p.Pro277Leu | missense_variant | 5/7 | 1 | NM_001114123.3 | P1 | |
ELK1 | ENST00000247161.7 | c.830C>T | p.Pro277Leu | missense_variant | 4/6 | 1 | P1 | ||
ELK1 | ENST00000343894.8 | c.271-955C>T | intron_variant | 1 |
Frequencies
GnomAD3 genomes Cov.: 23
GnomAD3 exomes AF: 0.0000338 AC: 6AN: 177467Hom.: 0 AF XY: 0.0000306 AC XY: 2AN XY: 65293
GnomAD4 exome AF: 0.0000319 AC: 35AN: 1097634Hom.: 0 Cov.: 32 AF XY: 0.0000193 AC XY: 7AN XY: 363210
GnomAD4 genome Cov.: 23
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jul 25, 2023 | The c.830C>T (p.P277L) alteration is located in exon 4 (coding exon 3) of the ELK1 gene. This alteration results from a C to T substitution at nucleotide position 830, causing the proline (P) at amino acid position 277 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