12-54399935-C-G
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_002205.5(ITGA5):āc.2656G>Cā(p.Gly886Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000214 in 1,613,864 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ).
Frequency
Consequence
NM_002205.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ITGA5 | NM_002205.5 | c.2656G>C | p.Gly886Arg | missense_variant | 26/30 | ENST00000293379.9 | |
GPR84-AS1 | NR_120486.1 | n.207-7462C>G | intron_variant, non_coding_transcript_variant | ||||
ITGA5 | XM_024448970.2 | c.1144G>C | p.Gly382Arg | missense_variant | 13/17 | ||
GPR84-AS1 | NR_120487.1 | n.207-7462C>G | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ITGA5 | ENST00000293379.9 | c.2656G>C | p.Gly886Arg | missense_variant | 26/30 | 1 | NM_002205.5 | P1 | |
GPR84-AS1 | ENST00000550474.5 | n.48-27922C>G | intron_variant, non_coding_transcript_variant | 4 | |||||
GPR84-AS1 | ENST00000552785.1 | n.106-7462C>G | intron_variant, non_coding_transcript_variant | 4 |
Frequencies
GnomAD3 genomes AF: 0.000289 AC: 44AN: 152186Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000402 AC: 101AN: 251342Hom.: 0 AF XY: 0.000368 AC XY: 50AN XY: 135848
GnomAD4 exome AF: 0.000207 AC: 302AN: 1461558Hom.: 0 Cov.: 30 AF XY: 0.000221 AC XY: 161AN XY: 727102
GnomAD4 genome AF: 0.000289 AC: 44AN: 152306Hom.: 0 Cov.: 32 AF XY: 0.000295 AC XY: 22AN XY: 74486
ClinVar
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Sep 10, 2018 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at