rs371352710
Variant summary
Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP4_StrongBP6_Very_StrongBS2
The NM_001103.4(ACTN2):c.1975-12C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000874 in 1,614,026 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_001103.4 intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -16 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
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ACTN2 | NM_001103.4 | c.1975-12C>T | intron_variant | Intron 16 of 20 | ENST00000366578.6 | NP_001094.1 | ||
ACTN2 | NM_001278343.2 | c.1975-12C>T | intron_variant | Intron 16 of 20 | NP_001265272.1 | |||
ACTN2 | NR_184402.1 | n.2347-12C>T | intron_variant | Intron 18 of 22 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000322 AC: 49AN: 152192Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000915 AC: 23AN: 251448Hom.: 0 AF XY: 0.0000662 AC XY: 9AN XY: 135902
GnomAD4 exome AF: 0.0000629 AC: 92AN: 1461834Hom.: 0 Cov.: 32 AF XY: 0.0000605 AC XY: 44AN XY: 727218
GnomAD4 genome AF: 0.000322 AC: 49AN: 152192Hom.: 0 Cov.: 33 AF XY: 0.000417 AC XY: 31AN XY: 74366
ClinVar
Submissions by phenotype
not specified Benign:4
This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -
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c.1975-12C>T in intron 16 of ACTN2: This variant is not expected to have clinica l significance because a C>T change at this position does not diverge from the s plice consensus sequence and is therefore unlikely to impact splicing. It has b een identified in 20/24030 African chromosomes by the Genome Aggregation Databas e (gnomAD, http://gnomad.broadinstitute.org/; dbSNP rs371352710). -
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Primary familial hypertrophic cardiomyopathy;C2677338:Dilated cardiomyopathy 1AA Benign:1
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Dilated cardiomyopathy 1AA Benign:1
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not provided Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at