chr1-100719897-A-T
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_001078.4(VCAM1):c.37A>T(p.Asn13Tyr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000273 in 1,611,320 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001078.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
VCAM1 | NM_001078.4 | c.37A>T | p.Asn13Tyr | missense_variant | 1/9 | ENST00000294728.7 | |
VCAM1 | NM_001199834.2 | c.37A>T | p.Asn13Tyr | missense_variant | 1/9 | ||
VCAM1 | NM_080682.3 | c.37A>T | p.Asn13Tyr | missense_variant | 1/8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
VCAM1 | ENST00000294728.7 | c.37A>T | p.Asn13Tyr | missense_variant | 1/9 | 1 | NM_001078.4 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000132 AC: 2AN: 152068Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000438 AC: 11AN: 250932Hom.: 0 AF XY: 0.0000442 AC XY: 6AN XY: 135614
GnomAD4 exome AF: 0.0000288 AC: 42AN: 1459252Hom.: 0 Cov.: 30 AF XY: 0.0000289 AC XY: 21AN XY: 725926
GnomAD4 genome AF: 0.0000132 AC: 2AN: 152068Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74278
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jun 18, 2021 | The c.37A>T (p.N13Y) alteration is located in exon 1 (coding exon 1) of the VCAM1 gene. This alteration results from a A to T substitution at nucleotide position 37, causing the asparagine (N) at amino acid position 13 to be replaced by a tyrosine (Y). 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