12-6935624-C-T
Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2
The NM_001940.4(ATN1):c.357C>T(p.Ser119Ser) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000781 in 1,613,912 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_001940.4 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -11 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000658 AC: 10AN: 152088Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000557 AC: 14AN: 251278Hom.: 1 AF XY: 0.0000442 AC XY: 6AN XY: 135812
GnomAD4 exome AF: 0.0000794 AC: 116AN: 1461706Hom.: 1 Cov.: 37 AF XY: 0.0000853 AC XY: 62AN XY: 727172
GnomAD4 genome AF: 0.0000657 AC: 10AN: 152206Hom.: 0 Cov.: 31 AF XY: 0.0000806 AC XY: 6AN XY: 74416
ClinVar
Submissions by phenotype
not provided Benign:1
ATN1: BP4, BP7 -
ATN1-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). -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at