rs1953758
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_207303.4(ATRNL1):c.2966G>A(p.Ser989Asn) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.968 in 1,613,860 control chromosomes in the GnomAD database, including 756,866 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_207303.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ATRNL1 | NM_207303.4 | c.2966G>A | p.Ser989Asn | missense_variant | 18/29 | ENST00000355044.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ATRNL1 | ENST00000355044.8 | c.2966G>A | p.Ser989Asn | missense_variant | 18/29 | 1 | NM_207303.4 | P1 | |
ATRNL1 | ENST00000526373.1 | c.356G>A | p.Ser119Asn | missense_variant | 3/6 | 5 | |||
ATRNL1 | ENST00000534530.5 | n.219G>A | non_coding_transcript_exon_variant | 2/6 | 4 | ||||
ATRNL1 | ENST00000650603.1 | c.2858G>A | p.Ser953Asn | missense_variant, NMD_transcript_variant | 18/30 |
Frequencies
GnomAD3 genomes ? AF: 0.968 AC: 147218AN: 152070Hom.: 71279 Cov.: 30
GnomAD3 exomes AF: 0.974 AC: 244790AN: 251330Hom.: 119243 AF XY: 0.974 AC XY: 132253AN XY: 135828
GnomAD4 exome AF: 0.968 AC: 1415477AN: 1461672Hom.: 685531 Cov.: 55 AF XY: 0.968 AC XY: 704200AN XY: 727148
GnomAD4 genome ? AF: 0.968 AC: 147333AN: 152188Hom.: 71335 Cov.: 30 AF XY: 0.969 AC XY: 72077AN XY: 74390
ClinVar
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Nov 05, 2021 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at