13-31143849-C-G
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_006644.4(HSPH1):āc.1659G>Cā(p.Gln553His) variant causes a missense change. The variant allele was found at a frequency of 0.0000123 in 1,459,520 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 (ā ).
Frequency
Consequence
NM_006644.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
HSPH1 | NM_006644.4 | c.1659G>C | p.Gln553His | missense_variant | Exon 12 of 18 | ENST00000320027.10 | NP_006635.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
HSPH1 | ENST00000320027.10 | c.1659G>C | p.Gln553His | missense_variant | Exon 12 of 18 | 1 | NM_006644.4 | ENSP00000318687.5 | ||
HSPH1 | ENST00000602786.5 | n.*1187G>C | non_coding_transcript_exon_variant | Exon 11 of 17 | 1 | ENSP00000473512.1 | ||||
HSPH1 | ENST00000602786.5 | n.*1187G>C | 3_prime_UTR_variant | Exon 11 of 17 | 1 | ENSP00000473512.1 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 exomes AF: 0.0000240 AC: 6AN: 249996Hom.: 0 AF XY: 0.0000370 AC XY: 5AN XY: 135142
GnomAD4 exome AF: 0.0000123 AC: 18AN: 1459520Hom.: 0 Cov.: 30 AF XY: 0.00000964 AC XY: 7AN XY: 726062
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1659G>C (p.Q553H) alteration is located in exon 12 (coding exon 12) of the HSPH1 gene. This alteration results from a G to C substitution at nucleotide position 1659, causing the glutamine (Q) at amino acid position 553 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