chr2-152720525-A-G
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_152522.7(ARL6IP6):c.401-8A>G variant causes a splice region, splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00281 in 1,613,046 control chromosomes in the GnomAD database, including 136 homozygotes. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Benign (★).
Frequency
Consequence
NM_152522.7 splice_region, splice_polypyrimidine_tract, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ARL6IP6 | NM_152522.7 | c.401-8A>G | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ENST00000326446.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ARL6IP6 | ENST00000326446.10 | c.401-8A>G | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_152522.7 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0154 AC: 2336AN: 152126Hom.: 68 Cov.: 33
GnomAD3 exomes AF: 0.00379 AC: 954AN: 251402Hom.: 28 AF XY: 0.00286 AC XY: 389AN XY: 135892
GnomAD4 exome AF: 0.00151 AC: 2199AN: 1460802Hom.: 69 Cov.: 31 AF XY: 0.00126 AC XY: 919AN XY: 726798
GnomAD4 genome AF: 0.0154 AC: 2338AN: 152244Hom.: 67 Cov.: 33 AF XY: 0.0146 AC XY: 1086AN XY: 74440
ClinVar
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Dec 31, 2019 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at