chr11-20919245-T-C
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_ModerateBP6_Moderate
The NM_006157.5(NELL1):c.677-7T>C variant causes a splice region, splice polypyrimidine tract, intron change. The variant allele was found at a frequency of 0.000122 in 1,552,376 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 2/2 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_006157.5 splice_region, splice_polypyrimidine_tract, intron
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 |
---|---|---|---|---|---|---|---|
NELL1 | NM_006157.5 | c.677-7T>C | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ENST00000357134.10 | |||
LOC105376585 | XR_931106.3 | n.84+7468A>G | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NELL1 | ENST00000357134.10 | c.677-7T>C | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_006157.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000645 AC: 98AN: 152032Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000141 AC: 34AN: 241140Hom.: 0 AF XY: 0.0000998 AC XY: 13AN XY: 130230
GnomAD4 exome AF: 0.0000657 AC: 92AN: 1400344Hom.: 0 Cov.: 23 AF XY: 0.0000601 AC XY: 42AN XY: 698976
GnomAD4 genome ? AF: 0.000645 AC: 98AN: 152032Hom.: 0 Cov.: 33 AF XY: 0.000566 AC XY: 42AN XY: 74268
ClinVar
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Al Jalila Children's Genomics Center, Al Jalila Childrens Speciality Hospital | Jan 02, 2020 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at