16-282759-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001176.4(ARHGDIG):c.623C>T(p.Thr208Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000516 in 1,609,080 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 Uncertain significance (★).
Frequency
Consequence
NM_001176.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ARHGDIG | ENST00000219409.8 | c.623C>T | p.Thr208Met | missense_variant | Exon 6 of 6 | 1 | NM_001176.4 | ENSP00000219409.3 | ||
ARHGDIG | ENST00000414650.1 | c.299C>T | p.Thr100Met | missense_variant | Exon 6 of 6 | 3 | ENSP00000410541.1 | |||
ARHGDIG | ENST00000477621.1 | n.1191C>T | non_coding_transcript_exon_variant | Exon 5 of 5 | 3 | |||||
ARHGDIG | ENST00000447871.5 | c.*71C>T | downstream_gene_variant | 5 | ENSP00000404435.1 |
Frequencies
GnomAD3 genomes AF: 0.0000460 AC: 7AN: 152074Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000821 AC: 20AN: 243458Hom.: 0 AF XY: 0.0000681 AC XY: 9AN XY: 132212
GnomAD4 exome AF: 0.0000522 AC: 76AN: 1456888Hom.: 0 Cov.: 36 AF XY: 0.0000469 AC XY: 34AN XY: 724448
GnomAD4 genome AF: 0.0000460 AC: 7AN: 152192Hom.: 0 Cov.: 32 AF XY: 0.0000403 AC XY: 3AN XY: 74408
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.623C>T (p.T208M) alteration is located in exon 6 (coding exon 6) of the ARHGDIG gene. This alteration results from a C to T substitution at nucleotide position 623, causing the threonine (T) at amino acid position 208 to be replaced by a methionine (M). 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