chr2-152718824-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_152522.7(ARL6IP6):c.200C>T(p.Pro67Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000186 in 1,609,604 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_152522.7 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ARL6IP6 | NM_152522.7 | c.200C>T | p.Pro67Leu | missense_variant | 1/4 | ENST00000326446.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ARL6IP6 | ENST00000326446.10 | c.200C>T | p.Pro67Leu | missense_variant | 1/4 | 1 | NM_152522.7 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000854 AC: 13AN: 152200Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000168 AC: 4AN: 237992Hom.: 0 AF XY: 0.0000154 AC XY: 2AN XY: 129780
GnomAD4 exome AF: 0.0000117 AC: 17AN: 1457404Hom.: 0 Cov.: 31 AF XY: 0.0000124 AC XY: 9AN XY: 724726
GnomAD4 genome AF: 0.0000854 AC: 13AN: 152200Hom.: 0 Cov.: 33 AF XY: 0.000134 AC XY: 10AN XY: 74354
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 12, 2021 | The c.200C>T (p.P67L) alteration is located in exon 1 (coding exon 1) of the ARL6IP6 gene. This alteration results from a C to T substitution at nucleotide position 200, causing the proline (P) at amino acid position 67 to be replaced by a leucine (L). 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