chr16-84479954-G-A
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_020947.4(MEAK7):c.1330C>T(p.Arg444Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00323 in 1,609,612 control chromosomes in the GnomAD database, including 16 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R444H) has been classified as Uncertain significance.
Frequency
Consequence
NM_020947.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MEAK7 | NM_020947.4 | c.1330C>T | p.Arg444Cys | missense_variant | 8/8 | ENST00000343629.11 | |
MEAK7 | XM_005256075.3 | c.1330C>T | p.Arg444Cys | missense_variant | 9/9 | ||
MEAK7 | XM_017023511.2 | c.1330C>T | p.Arg444Cys | missense_variant | 8/8 | ||
MEAK7 | XM_047434410.1 | c.1330C>T | p.Arg444Cys | missense_variant | 8/8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MEAK7 | ENST00000343629.11 | c.1330C>T | p.Arg444Cys | missense_variant | 8/8 | 1 | NM_020947.4 | P1 | |
MEAK7 | ENST00000566995.5 | c.*744C>T | 3_prime_UTR_variant, NMD_transcript_variant | 9/9 | 5 | ||||
MEAK7 | ENST00000570036.5 | c.*1385C>T | 3_prime_UTR_variant, NMD_transcript_variant | 9/9 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.00268 AC: 408AN: 152228Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00255 AC: 635AN: 249320Hom.: 2 AF XY: 0.00266 AC XY: 359AN XY: 134750
GnomAD4 exome AF: 0.00328 AC: 4783AN: 1457266Hom.: 16 Cov.: 31 AF XY: 0.00324 AC XY: 2346AN XY: 724684
GnomAD4 genome ? AF: 0.00268 AC: 408AN: 152346Hom.: 0 Cov.: 32 AF XY: 0.00272 AC XY: 203AN XY: 74496
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Dec 31, 2019 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at