chr11-3667573-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_020402.4(CHRNA10):c.554G>A(p.Arg185Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000988 in 1,558,062 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 11/16 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 Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CHRNA10 | NM_020402.4 | c.554G>A | p.Arg185Gln | missense_variant | 4/5 | ENST00000250699.2 | |
CHRNA10 | NM_001303034.2 | c.-65G>A | 5_prime_UTR_variant | 4/5 | |||
CHRNA10 | NM_001303035.2 | c.-65G>A | 5_prime_UTR_variant | 4/5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CHRNA10 | ENST00000250699.2 | c.554G>A | p.Arg185Gln | missense_variant | 4/5 | 1 | NM_020402.4 | P1 | |
CHRNA10 | ENST00000534359.1 | c.7G>A | p.Gly3Ser | missense_variant | 4/5 | 1 | |||
CHRNA10 | ENST00000526599.1 | c.*325G>A | 3_prime_UTR_variant, NMD_transcript_variant | 4/5 | 1 |
Frequencies
GnomAD3 genomes AF: 0.000145 AC: 22AN: 152158Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000899 AC: 14AN: 155784Hom.: 0 AF XY: 0.0000348 AC XY: 3AN XY: 86276
GnomAD4 exome AF: 0.0000939 AC: 132AN: 1405794Hom.: 0 Cov.: 32 AF XY: 0.0000876 AC XY: 61AN XY: 696574
GnomAD4 genome AF: 0.000144 AC: 22AN: 152268Hom.: 0 Cov.: 33 AF XY: 0.000121 AC XY: 9AN XY: 74458
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jul 14, 2022 | The c.554G>A (p.R185Q) alteration is located in exon 4 (coding exon 4) of the CHRNA10 gene. This alteration results from a G to A substitution at nucleotide position 554, causing the arginine (R) at amino acid position 185 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