rs538856434
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS1
The NM_000245.4(MET):c.2731-8A>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 0.0000167 in 1,613,606 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 Likely benign (★).
Frequency
Consequence
NM_000245.4 splice_region, splice_polypyrimidine_tract, intron
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 |
---|---|---|---|---|---|---|---|
MET | NM_000245.4 | c.2731-8A>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ENST00000397752.8 | |||
MET | NM_001127500.3 | c.2785-8A>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ||||
MET | NM_001324402.2 | c.1441-8A>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ||||
MET | XM_011516223.2 | c.2788-8A>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MET | ENST00000397752.8 | c.2731-8A>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_000245.4 | P3 | |||
MET | ENST00000318493.11 | c.2785-8A>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 1 | A2 | ||||
MET | ENST00000436117.3 | c.*336-8A>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant, NMD_transcript_variant | 1 | |||||
MET | ENST00000454623.1 | c.127-8A>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.0000394 AC: 6AN: 152162Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000441 AC: 11AN: 249178Hom.: 0 AF XY: 0.0000222 AC XY: 3AN XY: 135174
GnomAD4 exome AF: 0.0000144 AC: 21AN: 1461326Hom.: 1 Cov.: 32 AF XY: 0.00000550 AC XY: 4AN XY: 726962
GnomAD4 genome ? AF: 0.0000394 AC: 6AN: 152280Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74458
ClinVar
Submissions by phenotype
Renal cell carcinoma Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 24, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at