22-45387016-G-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 0P and 2B. BP4_Moderate
The NM_148674.5(SMC1B):c.1762C>T(p.Leu588Phe) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000616 in 1,461,412 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/18 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_148674.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SMC1B | NM_148674.5 | c.1762C>T | p.Leu588Phe | missense_variant | 11/25 | ENST00000357450.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SMC1B | ENST00000357450.9 | c.1762C>T | p.Leu588Phe | missense_variant | 11/25 | 5 | NM_148674.5 | P1 | |
SMC1B | ENST00000404354.3 | c.1762C>T | p.Leu588Phe | missense_variant | 11/23 | 1 |
Frequencies
GnomAD3 genomes ? Cov.: 33
GnomAD3 exomes AF: 0.00000802 AC: 2AN: 249412Hom.: 0 AF XY: 0.00000739 AC XY: 1AN XY: 135324
GnomAD4 exome AF: 0.00000616 AC: 9AN: 1461412Hom.: 0 Cov.: 30 AF XY: 0.00000825 AC XY: 6AN XY: 727018
GnomAD4 genome ? Cov.: 33
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 26, 2022 | The c.1762C>T (p.L588F) alteration is located in exon 11 (coding exon 11) of the SMC1B gene. This alteration results from a C to T substitution at nucleotide position 1762, causing the leucine (L) at amino acid position 588 to be replaced by a phenylalanine (F). 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