chr10-106579159-T-C
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_052918.5(SORCS1):c.3371+210A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0206 in 1,614,072 control chromosomes in the GnomAD database, including 2,201 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.039 ( 315 hom., cov: 32)
Exomes 𝑓: 0.019 ( 1886 hom. )
Consequence
SORCS1
NM_052918.5 intron
NM_052918.5 intron
Scores
12
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.0930
Genes affected
SORCS1 (HGNC:16697): (sortilin related VPS10 domain containing receptor 1) This gene encodes one family member of vacuolar protein sorting 10 (VPS10) domain-containing receptor proteins. The VPS10 domain name comes from the yeast carboxypeptidase Y sorting receptor Vps10 protein. Members of this gene family are large with many exons but the CDS lengths are usually less than 3700 nt. Very large introns typically separate the exons encoding the VPS10 domain; the remaining exons are separated by much smaller-sized introns. These genes are strongly expressed in the central nervous system. Two of the five family members (sortilin and sortilin-related receptor) are synthesized as preproproteins; it is not yet known if this encoded protein is also a preproprotein. Alternatively spliced transcript variants encoding different isoforms have been identified. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (MetaRNN=0.0029719472).
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.236 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SORCS1 | NM_052918.5 | c.3371+210A>G | intron_variant | ENST00000263054.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SORCS1 | ENST00000263054.11 | c.3371+210A>G | intron_variant | 1 | NM_052918.5 | P1 | |||
SORCS1 | ENST00000369698.6 | c.2198A>G | p.Asn733Ser | missense_variant | 18/19 | 5 | |||
SORCS1 | ENST00000452214.5 | c.509A>G | p.Asn170Ser | missense_variant | 5/6 | 3 | |||
SORCS1 | ENST00000473866.1 | n.352A>G | non_coding_transcript_exon_variant | 4/4 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.0390 AC: 5932AN: 152116Hom.: 315 Cov.: 32
GnomAD3 genomes
?
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GnomAD3 exomes AF: 0.0513 AC: 12905AN: 251332Hom.: 998 AF XY: 0.0468 AC XY: 6352AN XY: 135824
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GnomAD4 exome AF: 0.0187 AC: 27301AN: 1461836Hom.: 1886 Cov.: 31 AF XY: 0.0191 AC XY: 13917AN XY: 727220
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GnomAD4 genome ? AF: 0.0390 AC: 5936AN: 152236Hom.: 315 Cov.: 32 AF XY: 0.0436 AC XY: 3249AN XY: 74438
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252
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5555
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ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Benign
D
LIST_S2
Benign
T;T;T
MetaRNN
Benign
T;T;T
MetaSVM
Benign
T
MutationTaster
Benign
P;P;P
PrimateAI
Benign
T
Sift4G
Benign
T;T;T
Vest4
0.027
MPC
0.20
ClinPred
T
GERP RS
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at