chr1-201488917-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_004078.3(CSRP1):c.349G>A(p.Glu117Lys) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000479 in 1,461,824 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_004078.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CSRP1 | NM_004078.3 | c.349G>A | p.Glu117Lys | missense_variant | Exon 4 of 6 | ENST00000340006.7 | NP_004069.1 | |
CSRP1 | NM_001193571.2 | c.349G>A | p.Glu117Lys | missense_variant | Exon 4 of 6 | NP_001180500.1 | ||
CSRP1 | NM_001193572.2 | c.349G>A | p.Glu117Lys | missense_variant | Exon 4 of 6 | NP_001180501.1 | ||
CSRP1 | NM_001193570.2 | c.349G>A | p.Glu117Lys | missense_variant | Exon 4 of 6 | NP_001180499.1 |
Ensembl
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 exomes AF: 0.0000119 AC: 3AN: 251380Hom.: 0 AF XY: 0.0000147 AC XY: 2AN XY: 135882
GnomAD4 exome AF: 0.00000479 AC: 7AN: 1461824Hom.: 0 Cov.: 30 AF XY: 0.00000413 AC XY: 3AN XY: 727222
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.349G>A (p.E117K) alteration is located in exon 4 (coding exon 3) of the CSRP1 gene. This alteration results from a G to A substitution at nucleotide position 349, causing the glutamic acid (E) at amino acid position 117 to be replaced by a lysine (K). 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