chr11-3667570-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_020402.4(CHRNA10):c.557C>T(p.Pro186Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000641 in 1,558,976 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_020402.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CHRNA10 | NM_020402.4 | c.557C>T | p.Pro186Leu | missense_variant | 4/5 | ENST00000250699.2 | |
CHRNA10 | NM_001303034.2 | c.-62C>T | 5_prime_UTR_variant | 4/5 | |||
CHRNA10 | NM_001303035.2 | c.-62C>T | 5_prime_UTR_variant | 4/5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CHRNA10 | ENST00000250699.2 | c.557C>T | p.Pro186Leu | missense_variant | 4/5 | 1 | NM_020402.4 | P1 | |
CHRNA10 | ENST00000534359.1 | c.10C>T | p.Arg4Cys | missense_variant | 4/5 | 1 | |||
CHRNA10 | ENST00000526599.1 | c.*328C>T | 3_prime_UTR_variant, NMD_transcript_variant | 4/5 | 1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000131 AC: 2AN: 152146Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000127 AC: 2AN: 157316Hom.: 0 AF XY: 0.0000115 AC XY: 1AN XY: 87276
GnomAD4 exome AF: 0.00000569 AC: 8AN: 1406830Hom.: 0 Cov.: 32 AF XY: 0.00000861 AC XY: 6AN XY: 697236
GnomAD4 genome ? AF: 0.0000131 AC: 2AN: 152146Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 74332
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jun 27, 2022 | The c.557C>T (p.P186L) alteration is located in exon 4 (coding exon 4) of the CHRNA10 gene. This alteration results from a C to T substitution at nucleotide position 557, causing the proline (P) at amino acid position 186 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