chr1-233353961-G-T
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_032435.3(MAP3K21):c.1135+6G>T variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.439 in 1,420,880 control chromosomes in the GnomAD database, including 118,783 homozygotes. In-silico tool predicts a benign outcome for this variant. 1/1 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_032435.3 splice_region, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
MAP3K21 | ENST00000366624.8 | c.1135+6G>T | splice_region_variant, intron_variant | Intron 3 of 9 | 1 | NM_032435.3 | ENSP00000355583.3 | |||
MAP3K21 | ENST00000366623.7 | c.1135+6G>T | splice_region_variant, intron_variant | Intron 3 of 5 | 1 | ENSP00000355582.3 |
Frequencies
GnomAD3 genomes AF: 0.441 AC: 66713AN: 151292Hom.: 15055 Cov.: 32
GnomAD3 exomes AF: 0.542 AC: 100085AN: 184532Hom.: 23009 AF XY: 0.538 AC XY: 53413AN XY: 99214
GnomAD4 exome AF: 0.439 AC: 556859AN: 1269478Hom.: 103691 Cov.: 37 AF XY: 0.442 AC XY: 276833AN XY: 626708
GnomAD4 genome AF: 0.441 AC: 66804AN: 151402Hom.: 15092 Cov.: 32 AF XY: 0.443 AC XY: 32735AN XY: 73918
ClinVar
Submissions by phenotype
not provided Benign:2
Benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Aug 08, 2018 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at