rs72665660
Variant names:
Your query was ambiguous. Multiple possible variants found:
Variant summary
Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_020159.5(SMARCAD1):c.368+106C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000292 in 342,116 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 0.0 ( 0 hom., cov: 18)
Exomes 𝑓: 0.0000029 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
SMARCAD1
NM_020159.5 intron
NM_020159.5 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -1.31
Publications
0 publications found
Genes affected
SMARCAD1 (HGNC:18398): (SWI/SNF-related, matrix-associated actin-dependent regulator of chromatin, subfamily a, containing DEAD/H box 1) This gene encodes a member of the SNF subfamily of helicase proteins. The encoded protein plays a critical role in the restoration of heterochromatin organization and propagation of epigenetic patterns following DNA replication by mediating histone H3/H4 deacetylation. Mutations in this gene are associated with adermatoglyphia. Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene. [provided by RefSeq, Dec 2011]
SMARCAD1 Gene-Disease associations (from GenCC):
- ectodermal dysplasia syndromeInheritance: AD Classification: DEFINITIVE Submitted by: Illumina
- isolated congenital adermatoglyphiaInheritance: AD Classification: STRONG, SUPPORTIVE Submitted by: Labcorp Genetics (formerly Invitae), Orphanet
- palmoplantar keratoderma-sclerodactyly syndromeInheritance: AD Classification: MODERATE, SUPPORTIVE Submitted by: Orphanet, G2P
- absence of fingerprints-congenital milia syndromeInheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
Genome browser will be placed here
ACMG classification
Classification was made for transcript
Our verdict: Likely_benign. The variant received -2 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.9).
Variant Effect in Transcripts
ACMG analysis was done for transcript: NM_020159.5. You can select a different transcript below to see updated ACMG assignments.
RefSeq Transcripts
| Sel. | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| SMARCAD1 | NM_020159.5 | MANE Select | c.368+106C>A | intron | N/A | NP_064544.2 | Q9H4L7-1 | ||
| SMARCAD1 | NM_001128429.3 | c.368+106C>A | intron | N/A | NP_001121901.1 | Q9H4L7-2 | |||
| SMARCAD1 | NM_001128430.2 | c.368+106C>A | intron | N/A | NP_001121902.1 | Q9H4L7-2 |
Ensembl Transcripts
| Sel. | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| SMARCAD1 | ENST00000354268.9 | TSL:1 MANE Select | c.368+106C>A | intron | N/A | ENSP00000346217.4 | Q9H4L7-1 | ||
| SMARCAD1 | ENST00000359052.8 | TSL:1 | c.368+106C>A | intron | N/A | ENSP00000351947.4 | Q9H4L7-2 | ||
| SMARCAD1 | ENST00000457823.6 | TSL:1 | c.368+106C>A | intron | N/A | ENSP00000415576.2 | Q9H4L7-2 |
Frequencies
GnomAD3 genomes 0.00 AC: 0AN: 124022Hom.: 0 Cov.: 18
GnomAD3 genomes
AF:
AC:
0
AN:
124022
Hom.:
Cov.:
18
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:
GnomAD4 exome AF: 0.00000292 AC: 1AN: 342116Hom.: 0 AF XY: 0.00000545 AC XY: 1AN XY: 183378 show subpopulations ⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.
GnomAD4 exome
AF:
AC:
1
AN:
342116
Hom.:
AF XY:
AC XY:
1
AN XY:
183378
show subpopulations
⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.
African (AFR)
AF:
AC:
0
AN:
8428
American (AMR)
AF:
AC:
0
AN:
11970
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
9720
East Asian (EAS)
AF:
AC:
0
AN:
20248
South Asian (SAS)
AF:
AC:
0
AN:
32070
European-Finnish (FIN)
AF:
AC:
0
AN:
20974
Middle Eastern (MID)
AF:
AC:
0
AN:
1310
European-Non Finnish (NFE)
AF:
AC:
1
AN:
219538
Other (OTH)
AF:
AC:
0
AN:
17858
⚠️ The allele balance in gnomAD4 Exomes is highly skewed from 0.5 (p-value = 0), which strongly suggests a high chance of mosaicism in these individuals.
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.225
Heterozygous variant carriers
0
0
1
1
2
2
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
GnomAD4 genome 0.00 AC: 0AN: 124024Hom.: 0 Cov.: 18 AF XY: 0.00 AC XY: 0AN XY: 58044
GnomAD4 genome
Data not reliable, filtered out with message: AC0
AF:
AC:
0
AN:
124024
Hom.:
Cov.:
18
AF XY:
AC XY:
0
AN XY:
58044
African (AFR)
AF:
AC:
0
AN:
32570
American (AMR)
AF:
AC:
0
AN:
11286
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
3224
East Asian (EAS)
AF:
AC:
0
AN:
4458
South Asian (SAS)
AF:
AC:
0
AN:
4056
European-Finnish (FIN)
AF:
AC:
0
AN:
4082
Middle Eastern (MID)
AF:
AC:
0
AN:
202
European-Non Finnish (NFE)
AF:
AC:
0
AN:
61614
Other (OTH)
AF:
AC:
0
AN:
1696
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
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
Publications
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