chr10-77806906-C-T
Variant summary
Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP4_StrongBP6_Very_StrongBS2
The NM_004747.4(DLG5):c.4819G>A(p.Asp1607Asn) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00448 in 1,613,758 control chromosomes in the GnomAD database, including 24 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_004747.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -16 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DLG5 | NM_004747.4 | c.4819G>A | p.Asp1607Asn | missense_variant | 26/32 | ENST00000372391.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DLG5 | ENST00000372391.7 | c.4819G>A | p.Asp1607Asn | missense_variant | 26/32 | 1 | NM_004747.4 | P1 |
Frequencies
GnomAD3 genomes AF: 0.00370 AC: 563AN: 152228Hom.: 1 Cov.: 32
GnomAD3 exomes AF: 0.00333 AC: 836AN: 251408Hom.: 3 AF XY: 0.00322 AC XY: 437AN XY: 135870
GnomAD4 exome AF: 0.00456 AC: 6660AN: 1461412Hom.: 23 Cov.: 36 AF XY: 0.00443 AC XY: 3221AN XY: 726922
GnomAD4 genome AF: 0.00369 AC: 562AN: 152346Hom.: 1 Cov.: 32 AF XY: 0.00341 AC XY: 254AN XY: 74492
ClinVar
Submissions by phenotype
not provided Benign:2
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Dec 01, 2022 | DLG5: BP4, BS2 - |
Likely 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