7-75541938-C-T
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP4BS2
The NM_005338.7(HIP1):c.2933G>A(p.Arg978His) variant causes a missense change. The variant allele was found at a frequency of 0.0000316 in 1,613,382 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R978C) has been classified as Uncertain significance.
Frequency
Consequence
NM_005338.7 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
HIP1 | NM_005338.7 | c.2933G>A | p.Arg978His | missense_variant | 29/31 | ENST00000336926.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
HIP1 | ENST00000336926.11 | c.2933G>A | p.Arg978His | missense_variant | 29/31 | 1 | NM_005338.7 | P1 | |
HIP1 | ENST00000616821.4 | c.2846G>A | p.Arg949His | missense_variant | 29/31 | 1 | |||
HIP1 | ENST00000434438.6 | c.2780G>A | p.Arg927His | missense_variant | 27/29 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000263 AC: 4AN: 152158Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000123 AC: 31AN: 251478Hom.: 0 AF XY: 0.0000957 AC XY: 13AN XY: 135912
GnomAD4 exome AF: 0.0000322 AC: 47AN: 1461224Hom.: 0 Cov.: 29 AF XY: 0.0000248 AC XY: 18AN XY: 726984
GnomAD4 genome ? AF: 0.0000263 AC: 4AN: 152158Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74328
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jun 21, 2022 | The c.2933G>A (p.R978H) alteration is located in exon 29 (coding exon 29) of the HIP1 gene. This alteration results from a G to A substitution at nucleotide position 2933, causing the arginine (R) at amino acid position 978 to be replaced by a histidine (H). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at