chr17-12980171-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_014859.6(ARHGAP44):c.1877C>T(p.Pro626Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000167 in 1,612,972 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 (★).
Frequency
Consequence
NM_014859.6 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 |
---|---|---|---|---|---|---|---|
ARHGAP44 | NM_014859.6 | c.1877C>T | p.Pro626Leu | missense_variant | 19/21 | ENST00000379672.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ARHGAP44 | ENST00000379672.10 | c.1877C>T | p.Pro626Leu | missense_variant | 19/21 | 1 | NM_014859.6 | P4 |
Frequencies
GnomAD3 genomes ? AF: 0.0000263 AC: 4AN: 152176Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000244 AC: 6AN: 245942Hom.: 0 AF XY: 0.0000149 AC XY: 2AN XY: 133994
GnomAD4 exome AF: 0.0000157 AC: 23AN: 1460796Hom.: 0 Cov.: 31 AF XY: 0.0000179 AC XY: 13AN XY: 726578
GnomAD4 genome ? AF: 0.0000263 AC: 4AN: 152176Hom.: 0 Cov.: 33 AF XY: 0.0000135 AC XY: 1AN XY: 74344
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 01, 2023 | The c.1877C>T (p.P626L) alteration is located in exon 19 (coding exon 19) of the ARHGAP44 gene. This alteration results from a C to T substitution at nucleotide position 1877, causing the proline (P) at amino acid position 626 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