rs201587159
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_StrongBP6BS2
The NM_021175.4(HAMP):c.150+7G>A variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00109 in 1,612,606 control chromosomes in the GnomAD database, including 5 homozygotes. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_021175.4 splice_region, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -9 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
HAMP | NM_021175.4 | c.150+7G>A | splice_region_variant, intron_variant | ENST00000222304.5 | NP_066998.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
HAMP | ENST00000222304.5 | c.150+7G>A | splice_region_variant, intron_variant | 1 | NM_021175.4 | ENSP00000222304 | P1 | |||
HAMP | ENST00000598398.5 | c.150+7G>A | splice_region_variant, intron_variant | 2 | ENSP00000471894 | P1 | ||||
HAMP | ENST00000593580.1 | n.2339G>A | non_coding_transcript_exon_variant | 1/1 |
Frequencies
GnomAD3 genomes AF: 0.00106 AC: 161AN: 152092Hom.: 1 Cov.: 31
GnomAD3 exomes AF: 0.00150 AC: 378AN: 251416Hom.: 1 AF XY: 0.00160 AC XY: 217AN XY: 135888
GnomAD4 exome AF: 0.00109 AC: 1598AN: 1460396Hom.: 4 Cov.: 30 AF XY: 0.00118 AC XY: 858AN XY: 726610
GnomAD4 genome AF: 0.00106 AC: 162AN: 152210Hom.: 1 Cov.: 31 AF XY: 0.00118 AC XY: 88AN XY: 74420
ClinVar
Submissions by phenotype
Hemochromatosis type 2B Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jan 13, 2018 | This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score, this variant could not be ruled out of causing disease and therefore its association with disease required further investigation. A literature search was performed for the gene, cDNA change, and amino acid change (if applicable). No publications were found based on this search. This variant was therefore classified as a variant of unknown significance for this disease. - |
Hereditary hemochromatosis Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jan 31, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at