1-235979111-C-T
Variant summary
Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP4_StrongBP6_Very_StrongBS2
The NM_002508.3(NID1):c.3510-4G>A variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0114 in 1,586,162 control chromosomes in the GnomAD database, including 158 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_002508.3 splice_region, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -16 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
NID1 | ENST00000264187.7 | c.3510-4G>A | splice_region_variant, intron_variant | Intron 18 of 19 | 1 | NM_002508.3 | ENSP00000264187.6 | |||
NID1 | ENST00000366595.7 | c.3111-4G>A | splice_region_variant, intron_variant | Intron 15 of 16 | 1 | ENSP00000355554.3 |
Frequencies
GnomAD3 genomes AF: 0.00897 AC: 1365AN: 152132Hom.: 12 Cov.: 32
GnomAD3 exomes AF: 0.00926 AC: 2323AN: 250866Hom.: 23 AF XY: 0.00904 AC XY: 1226AN XY: 135560
GnomAD4 exome AF: 0.0116 AC: 16680AN: 1433912Hom.: 146 Cov.: 26 AF XY: 0.0112 AC XY: 7991AN XY: 715272
GnomAD4 genome AF: 0.00897 AC: 1365AN: 152250Hom.: 12 Cov.: 32 AF XY: 0.00884 AC XY: 658AN XY: 74440
ClinVar
Submissions by phenotype
not provided Benign:2
NID1: BP4, BS1, BS2 -
- -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at