12-54397391-C-T
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP4BS2
The NM_002205.5(ITGA5):c.3040G>A(p.Gly1014Ser) variant causes a missense change. The variant allele was found at a frequency of 0.00000496 in 1,613,950 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. G1014D) has been classified as Uncertain significance.
Frequency
Consequence
NM_002205.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ITGA5 | NM_002205.5 | c.3040G>A | p.Gly1014Ser | missense_variant | 29/30 | ENST00000293379.9 | |
GPR84-AS1 | NR_120486.1 | n.207-10006C>T | intron_variant, non_coding_transcript_variant | ||||
ITGA5 | XM_024448970.2 | c.1528G>A | p.Gly510Ser | missense_variant | 16/17 | ||
GPR84-AS1 | NR_120487.1 | n.207-10006C>T | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ITGA5 | ENST00000293379.9 | c.3040G>A | p.Gly1014Ser | missense_variant | 29/30 | 1 | NM_002205.5 | P1 | |
GPR84-AS1 | ENST00000550474.5 | n.48-30466C>T | intron_variant, non_coding_transcript_variant | 4 | |||||
GPR84-AS1 | ENST00000552785.1 | n.106-10006C>T | intron_variant, non_coding_transcript_variant | 4 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152122Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000795 AC: 2AN: 251456Hom.: 0 AF XY: 0.0000147 AC XY: 2AN XY: 135902
GnomAD4 exome AF: 0.00000479 AC: 7AN: 1461828Hom.: 0 Cov.: 31 AF XY: 0.00000550 AC XY: 4AN XY: 727222
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152122Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74300
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 26, 2024 | The c.3040G>A (p.G1014S) alteration is located in exon 29 (coding exon 29) of the ITGA5 gene. This alteration results from a G to A substitution at nucleotide position 3040, causing the glycine (G) at amino acid position 1014 to be replaced by a serine (S). 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