chr1-176864291-T-C
Variant summary
Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_004319.3(ASTN1):c.3878A>G(p.Glu1293Gly) variant causes a missense change. The variant allele was found at a frequency of 0.00333 in 1,613,990 control chromosomes in the GnomAD database, including 22 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_004319.3 missense
Scores
Clinical Significance
Conservation
Publications
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ACMG classification
Our verdict: Benign. The variant received -10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ASTN1 | NM_004319.3 | c.3878A>G | p.Glu1293Gly | missense_variant | Exon 23 of 23 | ENST00000361833.7 | NP_004310.1 | |
ASTN1 | NM_001364856.2 | c.3902A>G | p.Glu1301Gly | missense_variant | Exon 23 of 23 | NP_001351785.1 | ||
ASTN1 | NM_001286164.2 | c.3647+4553A>G | intron_variant | Intron 22 of 22 | NP_001273093.1 | |||
ASTN1 | XM_017001341.3 | c.3671+4553A>G | intron_variant | Intron 22 of 22 | XP_016856830.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ASTN1 | ENST00000361833.7 | c.3878A>G | p.Glu1293Gly | missense_variant | Exon 23 of 23 | 1 | NM_004319.3 | ENSP00000354536.2 | ||
ASTN1 | ENST00000367657.7 | c.3647+4553A>G | intron_variant | Intron 22 of 22 | 1 | ENSP00000356629.3 | ||||
ASTN1 | ENST00000850957.1 | c.3902A>G | p.Glu1301Gly | missense_variant | Exon 23 of 23 | ENSP00000521041.1 |
Frequencies
GnomAD3 genomes AF: 0.00251 AC: 382AN: 152166Hom.: 1 Cov.: 32 show subpopulations
GnomAD2 exomes AF: 0.00236 AC: 592AN: 251024 AF XY: 0.00237 show subpopulations
GnomAD4 exome AF: 0.00341 AC: 4989AN: 1461706Hom.: 21 Cov.: 33 AF XY: 0.00332 AC XY: 2414AN XY: 727168 show subpopulations
GnomAD4 genome AF: 0.00251 AC: 382AN: 152284Hom.: 1 Cov.: 32 AF XY: 0.00240 AC XY: 179AN XY: 74462 show subpopulations
ClinVar
Submissions by phenotype
ASTN1-related disorder Benign:1
This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -
not provided Benign:1
ASTN1: BP4, BS2 -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at