rs2392221
Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP6BA1
The NM_001078.4(VCAM1):c.662-7C>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 0.15 in 1,606,466 control chromosomes in the GnomAD database, including 19,404 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 Lovd as Benign (no stars).
Frequency
Consequence
NM_001078.4 splice_region, splice_polypyrimidine_tract, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -13 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
VCAM1 | NM_001078.4 | c.662-7C>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ENST00000294728.7 | |||
VCAM1 | NM_001199834.2 | c.476-7C>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ||||
VCAM1 | NM_080682.3 | c.662-7C>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
VCAM1 | ENST00000294728.7 | c.662-7C>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_001078.4 | P1 |
Frequencies
GnomAD3 genomes AF: 0.141 AC: 21365AN: 151778Hom.: 1858 Cov.: 32
GnomAD3 exomes AF: 0.168 AC: 41793AN: 248244Hom.: 4167 AF XY: 0.164 AC XY: 22036AN XY: 134124
GnomAD4 exome AF: 0.151 AC: 219070AN: 1454568Hom.: 17541 Cov.: 32 AF XY: 0.150 AC XY: 108747AN XY: 722684
GnomAD4 genome AF: 0.141 AC: 21371AN: 151898Hom.: 1863 Cov.: 32 AF XY: 0.142 AC XY: 10536AN XY: 74218
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at