2-172088088-C-T
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_178120.5(DLX1):c.599C>T(p.Ala200Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00001 in 1,592,292 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_178120.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
DLX1 | NM_178120.5 | c.599C>T | p.Ala200Val | missense_variant | 3/3 | ENST00000361725.5 | NP_835221.2 | |
DLX1 | NM_001038493.2 | c.*9C>T | 3_prime_UTR_variant | 2/2 | NP_001033582.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
DLX1 | ENST00000361725.5 | c.599C>T | p.Ala200Val | missense_variant | 3/3 | 1 | NM_178120.5 | ENSP00000354478 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000263 AC: 4AN: 152150Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000172 AC: 4AN: 232496Hom.: 0 AF XY: 0.00000793 AC XY: 1AN XY: 126100
GnomAD4 exome AF: 0.00000833 AC: 12AN: 1440142Hom.: 0 Cov.: 31 AF XY: 0.00000978 AC XY: 7AN XY: 715490
GnomAD4 genome AF: 0.0000263 AC: 4AN: 152150Hom.: 0 Cov.: 33 AF XY: 0.0000269 AC XY: 2AN XY: 74316
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Nov 30, 2022 | The c.599C>T (p.A200V) alteration is located in exon 3 (coding exon 3) of the DLX1 gene. This alteration results from a C to T substitution at nucleotide position 599, causing the alanine (A) at amino acid position 200 to be replaced by a valine (V). 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