chr6-146685746-T-C
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_024694.4(ADGB):c.1229T>C(p.Ile410Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000255 in 1,529,960 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_024694.4 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 |
---|---|---|---|---|---|---|---|
ADGB | NM_024694.4 | c.1229T>C | p.Ile410Thr | missense_variant | 10/36 | ENST00000397944.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ADGB | ENST00000397944.8 | c.1229T>C | p.Ile410Thr | missense_variant | 10/36 | 5 | NM_024694.4 | P4 | |
ADGB | ENST00000493950.6 | c.*339T>C | 3_prime_UTR_variant, NMD_transcript_variant | 8/32 | 1 | ||||
ADGB | ENST00000681847.1 | c.1229T>C | p.Ile410Thr | missense_variant | 10/36 | A2 | |||
ADGB | ENST00000326929.8 | n.1270T>C | non_coding_transcript_exon_variant | 10/18 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000197 AC: 3AN: 152090Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000145 AC: 2AN: 137668Hom.: 0 AF XY: 0.0000137 AC XY: 1AN XY: 73124
GnomAD4 exome AF: 0.0000261 AC: 36AN: 1377870Hom.: 0 Cov.: 29 AF XY: 0.0000177 AC XY: 12AN XY: 679332
GnomAD4 genome ? AF: 0.0000197 AC: 3AN: 152090Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 74290
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 20, 2023 | The c.1229T>C (p.I410T) alteration is located in exon 10 (coding exon 10) of the ADGB gene. This alteration results from a T to C substitution at nucleotide position 1229, causing the isoleucine (I) at amino acid position 410 to be replaced by a threonine (T). 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