chr14-68874936-T-A
Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 1P and 14B. PP2BP4_StrongBP6_ModerateBS1BS2
The NM_001130004.2(ACTN1):c.2668A>T(p.Thr890Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0138 in 1,612,820 control chromosomes in the GnomAD database, including 205 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 (★). Synonymous variant affecting the same amino acid position (i.e. T890T) has been classified as Likely benign.
Frequency
Consequence
NM_001130004.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -13 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ACTN1 | NM_001130004.2 | c.2668A>T | p.Thr890Ser | missense_variant | 22/22 | ENST00000394419.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ACTN1 | ENST00000394419.9 | c.2668A>T | p.Thr890Ser | missense_variant | 22/22 | 1 | NM_001130004.2 | P3 |
Frequencies
GnomAD3 genomes AF: 0.0113 AC: 1715AN: 152096Hom.: 19 Cov.: 33
GnomAD3 exomes AF: 0.0111 AC: 2778AN: 249814Hom.: 27 AF XY: 0.0111 AC XY: 1500AN XY: 135324
GnomAD4 exome AF: 0.0140 AC: 20479AN: 1460606Hom.: 186 Cov.: 31 AF XY: 0.0138 AC XY: 10014AN XY: 726444
GnomAD4 genome AF: 0.0113 AC: 1715AN: 152214Hom.: 19 Cov.: 33 AF XY: 0.0107 AC XY: 799AN XY: 74414
ClinVar
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 31, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at