20-1578574-A-G
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_006065.5(SIRPB1):āc.197T>Cā(p.Met66Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000181 in 1,436,604 control chromosomes in the GnomAD database, including 3 homozygotes. In-silico tool predicts a benign outcome for this variant. 16/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_006065.5 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/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SIRPB1 | NM_006065.5 | c.197T>C | p.Met66Thr | missense_variant | 2/6 | ENST00000381605.9 | |
SIRPB1 | NM_001083910.4 | c.197T>C | p.Met66Thr | missense_variant | 2/4 | ||
SIRPB1 | NM_001330639.2 | c.194T>C | p.Met65Thr | missense_variant | 2/4 | ||
SIRPB1 | XM_005260641.4 | c.194T>C | p.Met65Thr | missense_variant | 2/6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SIRPB1 | ENST00000381605.9 | c.197T>C | p.Met66Thr | missense_variant | 2/6 | 1 | NM_006065.5 |
Frequencies
GnomAD3 genomes Cov.: 29
GnomAD3 exomes AF: 0.00000404 AC: 1AN: 247792Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 133920
GnomAD4 exome AF: 0.0000181 AC: 26AN: 1436604Hom.: 3 Cov.: 33 AF XY: 0.0000168 AC XY: 12AN XY: 714868
GnomAD4 genome Cov.: 29
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jun 02, 2023 | The c.197T>C (p.M66T) alteration is located in exon 2 (coding exon 2) of the SIRPB1 gene. This alteration results from a T to C substitution at nucleotide position 197, causing the methionine (M) at amino acid position 66 to be replaced by a threonine (T). 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