rs1553204449
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_000748.3(CHRNB2):āc.1336A>Gā(p.Ser446Gly) variant causes a missense, splice region change. The variant allele was found at a frequency of 0.00000144 in 1,384,874 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Uncertain significance (ā ). Synonymous variant affecting the same amino acid position (i.e. S446S) has been classified as Uncertain significance.
Frequency
Consequence
NM_000748.3 missense, splice_region
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CHRNB2 | NM_000748.3 | c.1336A>G | p.Ser446Gly | missense_variant, splice_region_variant | 5/6 | ENST00000368476.4 | |
CHRNB2 | XM_017000180.3 | c.826A>G | p.Ser276Gly | missense_variant, splice_region_variant | 2/3 | ||
CHRNB2 | XR_001736952.3 | n.1603A>G | splice_region_variant, non_coding_transcript_exon_variant | 5/7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CHRNB2 | ENST00000368476.4 | c.1336A>G | p.Ser446Gly | missense_variant, splice_region_variant | 5/6 | 1 | NM_000748.3 | P4 | |
CHRNB2 | ENST00000637900.1 | c.1342A>G | p.Ser448Gly | missense_variant, splice_region_variant | 5/6 | 5 | A1 | ||
CHRNB2 | ENST00000636034.1 | c.1336A>G | p.Ser446Gly | missense_variant, splice_region_variant, NMD_transcript_variant | 5/9 | 5 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD4 exome AF: 0.00000144 AC: 2AN: 1384874Hom.: 0 Cov.: 33 AF XY: 0.00000293 AC XY: 2AN XY: 683504
GnomAD4 genome ? Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Athena Diagnostics | Feb 15, 2017 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at