chr5-163483159-G-C
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_001142556.2(HMMR):āc.1672G>Cā(p.Asp558His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00166 in 1,610,694 control chromosomes in the GnomAD database, including 39 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ).
Frequency
Consequence
NM_001142556.2 missense
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 | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
HMMR | NM_001142556.2 | c.1672G>C | p.Asp558His | missense_variant | 14/18 | ENST00000393915.9 | NP_001136028.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
HMMR | ENST00000393915.9 | c.1672G>C | p.Asp558His | missense_variant | 14/18 | 1 | NM_001142556.2 | ENSP00000377492.4 |
Frequencies
GnomAD3 genomes AF: 0.00916 AC: 1394AN: 152140Hom.: 22 Cov.: 33
GnomAD3 exomes AF: 0.00219 AC: 540AN: 246932Hom.: 6 AF XY: 0.00164 AC XY: 219AN XY: 133810
GnomAD4 exome AF: 0.000876 AC: 1278AN: 1458436Hom.: 17 Cov.: 31 AF XY: 0.000754 AC XY: 547AN XY: 725656
GnomAD4 genome AF: 0.00916 AC: 1395AN: 152258Hom.: 22 Cov.: 33 AF XY: 0.00876 AC XY: 652AN XY: 74438
ClinVar
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Apr 26, 2018 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at