5-52939596-A-G
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_181501.2(ITGA1):āc.3085A>Gā(p.Asn1029Asp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000872 in 1,604,994 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_181501.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ITGA1 | NM_181501.2 | c.3085A>G | p.Asn1029Asp | missense_variant | 25/29 | ENST00000282588.7 | NP_852478.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ITGA1 | ENST00000282588.7 | c.3085A>G | p.Asn1029Asp | missense_variant | 25/29 | 1 | NM_181501.2 | ENSP00000282588 | P1 | |
ITGA2-AS1 | ENST00000662246.1 | n.232-7060T>C | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes AF: 0.0000591 AC: 9AN: 152212Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000121 AC: 3AN: 247694Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 134080
GnomAD4 exome AF: 0.00000344 AC: 5AN: 1452664Hom.: 0 Cov.: 29 AF XY: 0.00000277 AC XY: 2AN XY: 723316
GnomAD4 genome AF: 0.0000591 AC: 9AN: 152330Hom.: 0 Cov.: 33 AF XY: 0.0000537 AC XY: 4AN XY: 74490
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 14, 2023 | The c.3085A>G (p.N1029D) alteration is located in exon 25 (coding exon 25) of the ITGA1 gene. This alteration results from a A to G substitution at nucleotide position 3085, causing the asparagine (N) at amino acid position 1029 to be replaced by an aspartic acid (D). 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