3-72750648-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_018130.3(SHQ1):c.1370C>T(p.Ser457Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000684 in 1,461,422 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_018130.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SHQ1 | NM_018130.3 | c.1370C>T | p.Ser457Leu | missense_variant | 11/11 | ENST00000325599.13 | |
SHQ1 | XR_001740192.3 | n.1287-22805C>T | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SHQ1 | ENST00000325599.13 | c.1370C>T | p.Ser457Leu | missense_variant | 11/11 | 1 | NM_018130.3 | P1 | |
SHQ1 | ENST00000468371.5 | n.2653C>T | non_coding_transcript_exon_variant | 3/3 | 1 | ||||
SHQ1 | ENST00000463369.5 | c.1286C>T | p.Ser429Leu | missense_variant | 11/11 | 2 | |||
SHQ1 | ENST00000444040.6 | c.*1247C>T | 3_prime_UTR_variant, NMD_transcript_variant | 11/11 | 2 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 exomes AF: 0.00000400 AC: 1AN: 249812Hom.: 0 AF XY: 0.00000740 AC XY: 1AN XY: 135088
GnomAD4 exome AF: 0.00000684 AC: 10AN: 1461422Hom.: 0 Cov.: 32 AF XY: 0.0000110 AC XY: 8AN XY: 726990
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 02, 2024 | The c.1370C>T (p.S457L) alteration is located in exon 11 (coding exon 11) of the SHQ1 gene. This alteration results from a C to T substitution at nucleotide position 1370, causing the serine (S) at amino acid position 457 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