16-84480032-G-A
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_020947.4(MEAK7):c.1258-6C>T variant causes a splice region, splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000183 in 1,588,476 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Benign (★).
Frequency
Consequence
NM_020947.4 splice_region, splice_polypyrimidine_tract, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MEAK7 | NM_020947.4 | c.1258-6C>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ENST00000343629.11 | |||
MEAK7 | XM_005256075.3 | c.1258-6C>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ||||
MEAK7 | XM_017023511.2 | c.1258-6C>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ||||
MEAK7 | XM_047434410.1 | c.1258-6C>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MEAK7 | ENST00000343629.11 | c.1258-6C>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_020947.4 | P1 | |||
MEAK7 | ENST00000566995.5 | c.*672-6C>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant, NMD_transcript_variant | 5 | |||||
MEAK7 | ENST00000570036.5 | c.*1313-6C>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant, NMD_transcript_variant | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.000907 AC: 138AN: 152232Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000231 AC: 55AN: 237716Hom.: 0 AF XY: 0.000186 AC XY: 24AN XY: 128906
GnomAD4 exome AF: 0.000104 AC: 150AN: 1436126Hom.: 1 Cov.: 30 AF XY: 0.0000688 AC XY: 49AN XY: 711716
GnomAD4 genome ? AF: 0.000919 AC: 140AN: 152350Hom.: 0 Cov.: 32 AF XY: 0.000765 AC XY: 57AN XY: 74498
ClinVar
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Mar 30, 2018 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at