chr15-72474693-TGAGGAGGACAGCGGCGCCGAGGAG-T
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS2
The NM_005744.5(ARIH1):c.64_87delAGCGGCGCCGAGGAGGAGGAGGAC(p.Ser22_Asp29del) variant causes a conservative inframe deletion change. The variant allele was found at a frequency of 0.0000229 in 1,570,832 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_005744.5 conservative_inframe_deletion
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ARIH1 | ENST00000379887.9 | c.64_87delAGCGGCGCCGAGGAGGAGGAGGAC | p.Ser22_Asp29del | conservative_inframe_deletion | Exon 1 of 14 | 1 | NM_005744.5 | ENSP00000369217.4 | ||
ARIH1 | ENST00000564062.1 | c.58_81delAGCGGCGCCGAGGAGGAGGAGGAC | p.Ser20_Asp27del | conservative_inframe_deletion | Exon 1 of 4 | 3 | ENSP00000454774.1 | |||
TMEM202-AS1 | ENST00000565181.1 | n.452_475delCTCCTCGGCGCCGCTGTCCTCCTC | non_coding_transcript_exon_variant | Exon 1 of 1 | 6 | |||||
ARIH1 | ENST00000570085.5 | n.64_87delAGCGGCGCCGAGGAGGAGGAGGAC | non_coding_transcript_exon_variant | Exon 1 of 5 | 3 | ENSP00000456746.1 |
Frequencies
GnomAD3 genomes AF: 0.0000132 AC: 2AN: 151364Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000146 AC: 3AN: 205606Hom.: 0 AF XY: 0.0000177 AC XY: 2AN XY: 112972
GnomAD4 exome AF: 0.0000240 AC: 34AN: 1419468Hom.: 0 AF XY: 0.0000241 AC XY: 17AN XY: 705886
GnomAD4 genome AF: 0.0000132 AC: 2AN: 151364Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 73914
ClinVar
Submissions by phenotype
not provided Uncertain:1
This variant, c.64_87del, results in the deletion of 8 amino acid(s) of the ARIH1 protein (p.Ser22_Asp29del), but otherwise preserves the integrity of the reading frame. The frequency data for this variant in the population databases is considered unreliable, as metrics indicate poor data quality at this position in the gnomAD database. This variant has not been reported in the literature in individuals affected with ARIH1-related conditions. Experimental studies and prediction algorithms are not available or were not evaluated, and the functional significance of this variant is currently unknown. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at