chr21-29092569-A-G
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The ENST00000341618.8(MAP3K7CL):c.358A>G(p.Ser120Gly) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000217 in 1,613,966 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
ENST00000341618.8 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MAP3K7CL | NM_001286634.2 | c.358A>G | p.Ser120Gly | missense_variant | 5/8 | ||
MAP3K7CL | NM_001371369.1 | c.358A>G | p.Ser120Gly | missense_variant | 6/9 | ||
MAP3K7CL | NM_020152.4 | c.358A>G | p.Ser120Gly | missense_variant | 7/10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MAP3K7CL | ENST00000341618.8 | c.358A>G | p.Ser120Gly | missense_variant | 5/8 | 1 | |||
MAP3K7CL | ENST00000399947.6 | c.358A>G | p.Ser120Gly | missense_variant | 6/9 | 1 | |||
MAP3K7CL | ENST00000496779.5 | n.806A>G | non_coding_transcript_exon_variant | 6/7 | 1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000131 AC: 2AN: 152188Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000398 AC: 10AN: 251480Hom.: 0 AF XY: 0.0000515 AC XY: 7AN XY: 135918
GnomAD4 exome AF: 0.0000226 AC: 33AN: 1461778Hom.: 0 Cov.: 30 AF XY: 0.0000206 AC XY: 15AN XY: 727156
GnomAD4 genome ? AF: 0.0000131 AC: 2AN: 152188Hom.: 0 Cov.: 33 AF XY: 0.0000134 AC XY: 1AN XY: 74356
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 22, 2023 | The c.358A>G (p.S120G) alteration is located in exon 6 (coding exon 4) of the MAP3K7CL gene. This alteration results from a A to G substitution at nucleotide position 358, causing the serine (S) at amino acid position 120 to be replaced by a glycine (G). 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