13-31139080-T-C
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_006644.4(HSPH1):āc.2008A>Gā(p.Thr670Ala) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000391 in 1,612,298 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict 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.2008A>G | p.Thr670Ala | missense_variant | Exon 15 of 18 | ENST00000320027.10 | NP_006635.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
HSPH1 | ENST00000320027.10 | c.2008A>G | p.Thr670Ala | missense_variant | Exon 15 of 18 | 1 | NM_006644.4 | ENSP00000318687.5 | ||
HSPH1 | ENST00000602786.5 | n.*1536A>G | non_coding_transcript_exon_variant | Exon 14 of 17 | 1 | ENSP00000473512.1 | ||||
HSPH1 | ENST00000602786.5 | n.*1536A>G | 3_prime_UTR_variant | Exon 14 of 17 | 1 | ENSP00000473512.1 |
Frequencies
GnomAD3 genomes AF: 0.00000658 AC: 1AN: 152088Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000399 AC: 1AN: 250822Hom.: 0 AF XY: 0.00000738 AC XY: 1AN XY: 135570
GnomAD4 exome AF: 0.0000425 AC: 62AN: 1460210Hom.: 0 Cov.: 30 AF XY: 0.0000413 AC XY: 30AN XY: 726470
GnomAD4 genome AF: 0.00000658 AC: 1AN: 152088Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74302
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.2008A>G (p.T670A) alteration is located in exon 15 (coding exon 15) of the HSPH1 gene. This alteration results from a A to G substitution at nucleotide position 2008, causing the threonine (T) at amino acid position 670 to be replaced by an alanine (A). 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