2-210298513-T-A
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 4P and 2B. PM1PM2BP4_Moderate
The NM_079420.3(MYL1):c.211A>T(p.Thr71Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000226 in 1,613,938 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_079420.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MYL1 | NM_079420.3 | c.211A>T | p.Thr71Ser | missense_variant | 3/7 | ENST00000352451.4 | |
MYL1 | NM_079422.3 | c.79A>T | p.Thr27Ser | missense_variant | 3/7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MYL1 | ENST00000352451.4 | c.211A>T | p.Thr71Ser | missense_variant | 3/7 | 1 | NM_079420.3 | ||
MYL1 | ENST00000341685.8 | c.79A>T | p.Thr27Ser | missense_variant | 3/7 | 1 | P1 | ||
MYL1 | ENST00000484290.1 | n.342A>T | non_coding_transcript_exon_variant | 4/6 | 5 | ||||
MYL1 | ENST00000496436.5 | n.314A>T | non_coding_transcript_exon_variant | 3/6 | 5 |
Frequencies
GnomAD3 genomes AF: 0.000112 AC: 17AN: 152150Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000637 AC: 16AN: 251270Hom.: 0 AF XY: 0.0000295 AC XY: 4AN XY: 135796
GnomAD4 exome AF: 0.000237 AC: 347AN: 1461788Hom.: 0 Cov.: 32 AF XY: 0.000235 AC XY: 171AN XY: 727192
GnomAD4 genome AF: 0.000112 AC: 17AN: 152150Hom.: 0 Cov.: 32 AF XY: 0.000108 AC XY: 8AN XY: 74316
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 18, 2023 | The c.211A>T (p.T71S) alteration is located in exon 3 (coding exon 3) of the MYL1 gene. This alteration results from a A to T substitution at nucleotide position 211, causing the threonine (T) at amino acid position 71 to be replaced by a serine (S). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at