chr8-42756013-A-G
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_004198.3(CHRNA6):āc.1186T>Cā(p.Phe396Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000211 in 1,614,148 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 16/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_004198.3 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 | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CHRNA6 | NM_004198.3 | c.1186T>C | p.Phe396Leu | missense_variant | 5/6 | ENST00000276410.7 | NP_004189.1 | |
CHRNA6 | NM_001199279.1 | c.1141T>C | p.Phe381Leu | missense_variant | 4/5 | NP_001186208.1 | ||
CHRNA6 | XM_047422396.1 | c.1186T>C | p.Phe396Leu | missense_variant | 6/7 | XP_047278352.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CHRNA6 | ENST00000276410.7 | c.1186T>C | p.Phe396Leu | missense_variant | 5/6 | 1 | NM_004198.3 | ENSP00000276410 | P1 | |
CHRNA6 | ENST00000534622.5 | c.1141T>C | p.Phe381Leu | missense_variant | 4/5 | 2 | ENSP00000433871 |
Frequencies
GnomAD3 genomes AF: 0.0000394 AC: 6AN: 152256Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000159 AC: 4AN: 251466Hom.: 0 AF XY: 0.0000221 AC XY: 3AN XY: 135902
GnomAD4 exome AF: 0.0000192 AC: 28AN: 1461892Hom.: 0 Cov.: 33 AF XY: 0.0000220 AC XY: 16AN XY: 727246
GnomAD4 genome AF: 0.0000394 AC: 6AN: 152256Hom.: 0 Cov.: 32 AF XY: 0.0000403 AC XY: 3AN XY: 74394
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | May 12, 2024 | The c.1186T>C (p.F396L) alteration is located in exon 5 (coding exon 5) of the CHRNA6 gene. This alteration results from a T to C substitution at nucleotide position 1186, causing the phenylalanine (F) at amino acid position 396 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