13-31137439-G-A
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_006644.4(HSPH1):c.2456C>T(p.Pro819Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000093 in 1,613,372 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 (★).
Frequency
Consequence
NM_006644.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
HSPH1 | NM_006644.4 | c.2456C>T | p.Pro819Leu | missense_variant | Exon 18 of 18 | ENST00000320027.10 | NP_006635.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
HSPH1 | ENST00000320027.10 | c.2456C>T | p.Pro819Leu | missense_variant | Exon 18 of 18 | 1 | NM_006644.4 | ENSP00000318687.5 | ||
HSPH1 | ENST00000602786.5 | n.*1984C>T | non_coding_transcript_exon_variant | Exon 17 of 17 | 1 | ENSP00000473512.1 | ||||
HSPH1 | ENST00000602786.5 | n.*1984C>T | 3_prime_UTR_variant | Exon 17 of 17 | 1 | ENSP00000473512.1 |
Frequencies
GnomAD3 genomes AF: 0.0000592 AC: 9AN: 151982Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000159 AC: 4AN: 250954Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135634
GnomAD4 exome AF: 0.00000411 AC: 6AN: 1461272Hom.: 0 Cov.: 31 AF XY: 0.00000275 AC XY: 2AN XY: 726974
GnomAD4 genome AF: 0.0000592 AC: 9AN: 152100Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74390
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.2456C>T (p.P819L) alteration is located in exon 18 (coding exon 18) of the HSPH1 gene. This alteration results from a C to T substitution at nucleotide position 2456, causing the proline (P) at amino acid position 819 to be replaced by a leucine (L). 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