chr19-35282638-C-T
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2BP4_ModerateBP6_ModerateBP7
The NM_021175.4(HAMP):c.61C>T(p.Leu21=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000458 in 1,614,018 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★). Synonymous variant affecting the same amino acid position (i.e. L21L) has been classified as Likely benign.
Frequency
Consequence
NM_021175.4 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
HAMP | NM_021175.4 | c.61C>T | p.Leu21= | synonymous_variant | 1/3 | ENST00000222304.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
HAMP | ENST00000222304.5 | c.61C>T | p.Leu21= | synonymous_variant | 1/3 | 1 | NM_021175.4 | P1 | |
HAMP | ENST00000598398.5 | c.61C>T | p.Leu21= | synonymous_variant | 2/4 | 2 | P1 | ||
HAMP | ENST00000593580.1 | n.122C>T | non_coding_transcript_exon_variant | 1/1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000591 AC: 9AN: 152270Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000199 AC: 50AN: 250992Hom.: 0 AF XY: 0.000199 AC XY: 27AN XY: 135680
GnomAD4 exome AF: 0.0000445 AC: 65AN: 1461748Hom.: 1 Cov.: 30 AF XY: 0.0000481 AC XY: 35AN XY: 727178
GnomAD4 genome ? AF: 0.0000591 AC: 9AN: 152270Hom.: 0 Cov.: 33 AF XY: 0.0000538 AC XY: 4AN XY: 74394
ClinVar
Submissions by phenotype
Hereditary hemochromatosis Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 09, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at