chr10-77806926-G-A
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_004747.4(DLG5):c.4799C>T(p.Ala1600Val) variant causes a missense, splice region change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00205 in 1,610,872 control chromosomes in the GnomAD database, including 68 homozygotes. In-silico tool predicts a benign outcome for this variant. 1/1 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Benign (★). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_004747.4 missense, splice_region
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 |
---|---|---|---|---|---|---|---|
DLG5 | NM_004747.4 | c.4799C>T | p.Ala1600Val | missense_variant, splice_region_variant | 26/32 | ENST00000372391.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DLG5 | ENST00000372391.7 | c.4799C>T | p.Ala1600Val | missense_variant, splice_region_variant | 26/32 | 1 | NM_004747.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0107 AC: 1623AN: 152164Hom.: 31 Cov.: 32
GnomAD3 exomes AF: 0.00267 AC: 672AN: 251270Hom.: 11 AF XY: 0.00203 AC XY: 275AN XY: 135802
GnomAD4 exome AF: 0.00115 AC: 1672AN: 1458590Hom.: 35 Cov.: 36 AF XY: 0.00101 AC XY: 734AN XY: 724906
GnomAD4 genome ? AF: 0.0107 AC: 1637AN: 152282Hom.: 33 Cov.: 32 AF XY: 0.00998 AC XY: 743AN XY: 74460
ClinVar
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Dec 31, 2019 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at