rs141414233
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_003922.4(HERC1):c.6225+4C>T variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0073 in 1,581,242 control chromosomes in the GnomAD database, including 44 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 Likely benign (★★).
Frequency
Consequence
NM_003922.4 splice_region, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
HERC1 | NM_003922.4 | c.6225+4C>T | splice_region_variant, intron_variant | ENST00000443617.7 | NP_003913.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
HERC1 | ENST00000443617.7 | c.6225+4C>T | splice_region_variant, intron_variant | 1 | NM_003922.4 | ENSP00000390158.2 | ||||
ENSG00000259589 | ENST00000559303.2 | n.287+8036G>A | intron_variant | 5 |
Frequencies
GnomAD3 genomes AF: 0.00544 AC: 827AN: 151908Hom.: 1 Cov.: 32
GnomAD3 exomes AF: 0.00527 AC: 1182AN: 224164Hom.: 5 AF XY: 0.00534 AC XY: 651AN XY: 121810
GnomAD4 exome AF: 0.00750 AC: 10722AN: 1429218Hom.: 43 Cov.: 29 AF XY: 0.00736 AC XY: 5227AN XY: 710032
GnomAD4 genome AF: 0.00544 AC: 827AN: 152024Hom.: 1 Cov.: 32 AF XY: 0.00486 AC XY: 361AN XY: 74282
ClinVar
Submissions by phenotype
not provided Benign:4
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jan 22, 2024 | - - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | May 13, 2019 | - - |
Likely benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Nov 01, 2024 | HERC1: BP4, BS2 - |
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | Dec 27, 2016 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at