2-210302408-A-T
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Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_079420.3(MYL1):c.160+80T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.386 in 1,347,298 control chromosomes in the GnomAD database, including 102,204 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.41 ( 12604 hom., cov: 32)
Exomes 𝑓: 0.38 ( 89600 hom. )
Consequence
MYL1
NM_079420.3 intron
NM_079420.3 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.452
Genes affected
MYL1 (HGNC:7582): (myosin light chain 1) Myosin is a hexameric ATPase cellular motor protein. It is composed of two heavy chains, two nonphosphorylatable alkali light chains, and two phosphorylatable regulatory light chains. This gene encodes a myosin alkali light chain expressed in fast skeletal muscle. Two transcript variants have been identified for this gene. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -20 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.54).
BP6
Variant 2-210302408-A-T is Benign according to our data. Variant chr2-210302408-A-T is described in ClinVar as [Benign]. Clinvar id is 1294855.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BA1
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.491 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MYL1 | NM_079420.3 | c.160+80T>A | intron_variant | ENST00000352451.4 | |||
MYL1 | NM_079422.3 | c.28+360T>A | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MYL1 | ENST00000352451.4 | c.160+80T>A | intron_variant | 1 | NM_079420.3 | ||||
MYL1 | ENST00000341685.8 | c.28+360T>A | intron_variant | 1 | P1 | ||||
MYL1 | ENST00000484290.1 | n.291+80T>A | intron_variant, non_coding_transcript_variant | 5 | |||||
MYL1 | ENST00000496436.5 | n.263+360T>A | intron_variant, non_coding_transcript_variant | 5 |
Frequencies
GnomAD3 genomes AF: 0.406 AC: 61577AN: 151802Hom.: 12563 Cov.: 32
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GnomAD4 exome AF: 0.383 AC: 458084AN: 1195378Hom.: 89600 AF XY: 0.385 AC XY: 229880AN XY: 597512
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GnomAD4 genome AF: 0.406 AC: 61681AN: 151920Hom.: 12604 Cov.: 32 AF XY: 0.415 AC XY: 30794AN XY: 74278
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ClinVar
Significance: Benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:2
Benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | May 13, 2021 | - - |
Computational scores
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Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at