rs7239096
Positions:
Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1
The NM_015295.3(SMCHD1):āc.399T>Cā(p.Tyr133=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00615 in 1,593,436 control chromosomes in the GnomAD database, including 510 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ā ).
Frequency
Genomes: š 0.033 ( 264 hom., cov: 32)
Exomes š: 0.0034 ( 246 hom. )
Consequence
SMCHD1
NM_015295.3 synonymous
NM_015295.3 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 1.60
Genes affected
SMCHD1 (HGNC:29090): (structural maintenance of chromosomes flexible hinge domain containing 1) This gene encodes a protein which contains a hinge region domain found in members of the SMC (structural maintenance of chromosomes) protein family. [provided by RefSeq, Dec 2011]
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -21 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.48).
BP6
?
Variant 18-2667006-T-C is Benign according to our data. Variant chr18-2667006-T-C is described in ClinVar as [Benign]. Clinvar id is 260646.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr18-2667006-T-C is described in Lovd as [Benign].
BP7
?
Synonymous conserved (PhyloP=1.6 with no splicing effect.
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.11 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SMCHD1 | NM_015295.3 | c.399T>C | p.Tyr133= | synonymous_variant | 3/48 | ENST00000320876.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SMCHD1 | ENST00000320876.11 | c.399T>C | p.Tyr133= | synonymous_variant | 3/48 | 5 | NM_015295.3 | P2 | |
SMCHD1 | ENST00000688342.1 | c.399T>C | p.Tyr133= | synonymous_variant | 3/47 | A2 | |||
SMCHD1 | ENST00000684915.1 | n.556T>C | non_coding_transcript_exon_variant | 3/14 |
Frequencies
GnomAD3 genomes ? AF: 0.0325 AC: 4950AN: 152192Hom.: 263 Cov.: 32
GnomAD3 genomes
?
AF:
AC:
4950
AN:
152192
Hom.:
Cov.:
32
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD3 exomes AF: 0.00797 AC: 1724AN: 216354Hom.: 79 AF XY: 0.00611 AC XY: 713AN XY: 116738
GnomAD3 exomes
AF:
AC:
1724
AN:
216354
Hom.:
AF XY:
AC XY:
713
AN XY:
116738
Gnomad AFR exome
AF:
Gnomad AMR exome
AF:
Gnomad ASJ exome
AF:
Gnomad EAS exome
AF:
Gnomad SAS exome
AF:
Gnomad FIN exome
AF:
Gnomad NFE exome
AF:
Gnomad OTH exome
AF:
GnomAD4 exome AF: 0.00336 AC: 4845AN: 1441126Hom.: 246 Cov.: 30 AF XY: 0.00290 AC XY: 2075AN XY: 715216
GnomAD4 exome
AF:
AC:
4845
AN:
1441126
Hom.:
Cov.:
30
AF XY:
AC XY:
2075
AN XY:
715216
Gnomad4 AFR exome
AF:
Gnomad4 AMR exome
AF:
Gnomad4 ASJ exome
AF:
Gnomad4 EAS exome
AF:
Gnomad4 SAS exome
AF:
Gnomad4 FIN exome
AF:
Gnomad4 NFE exome
AF:
Gnomad4 OTH exome
AF:
GnomAD4 genome ? AF: 0.0325 AC: 4957AN: 152310Hom.: 264 Cov.: 32 AF XY: 0.0321 AC XY: 2392AN XY: 74486
GnomAD4 genome
?
AF:
AC:
4957
AN:
152310
Hom.:
Cov.:
32
AF XY:
AC XY:
2392
AN XY:
74486
Gnomad4 AFR
AF:
Gnomad4 AMR
AF:
Gnomad4 ASJ
AF:
Gnomad4 EAS
AF:
Gnomad4 SAS
AF:
Gnomad4 FIN
AF:
Gnomad4 NFE
AF:
Gnomad4 OTH
AF:
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
14
AN:
3478
ClinVar
Significance: Benign
Submissions summary: Benign:3
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
Facioscapulohumeral muscular dystrophy 2 Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 22, 2024 | - - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jan 28, 2021 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at