1-182904427-A-G
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_030933.4(SHCBP1L):āc.1340T>Cā(p.Val447Ala) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00698 in 1,613,378 control chromosomes in the GnomAD database, including 77 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ).
Frequency
Consequence
NM_030933.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SHCBP1L | NM_030933.4 | c.1340T>C | p.Val447Ala | missense_variant | 8/10 | ENST00000367547.8 | NP_112195.2 | |
SHCBP1L | NM_001345928.2 | c.983T>C | p.Val328Ala | missense_variant | 9/11 | NP_001332857.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SHCBP1L | ENST00000367547.8 | c.1340T>C | p.Val447Ala | missense_variant | 8/10 | 1 | NM_030933.4 | ENSP00000356518 | P1 | |
SHCBP1L | ENST00000483655.5 | n.1283T>C | non_coding_transcript_exon_variant | 9/11 | 1 | |||||
SHCBP1L | ENST00000488956.5 | n.1800T>C | non_coding_transcript_exon_variant | 7/9 | 2 |
Frequencies
GnomAD3 genomes AF: 0.00654 AC: 993AN: 151790Hom.: 9 Cov.: 32
GnomAD3 exomes AF: 0.00671 AC: 1683AN: 250682Hom.: 12 AF XY: 0.00617 AC XY: 837AN XY: 135696
GnomAD4 exome AF: 0.00703 AC: 10268AN: 1461470Hom.: 68 Cov.: 32 AF XY: 0.00672 AC XY: 4884AN XY: 727016
GnomAD4 genome AF: 0.00654 AC: 993AN: 151908Hom.: 9 Cov.: 32 AF XY: 0.00738 AC XY: 548AN XY: 74224
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Apr 01, 2022 | SHCBP1L: BP4, BS2 - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at