chr11-6621604-C-T
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Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_003737.4(DCHS1):c.*175G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0112 in 766,734 control chromosomes in the GnomAD database, including 134 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Genomes: 𝑓 0.010 ( 13 hom., cov: 32)
Exomes 𝑓: 0.011 ( 121 hom. )
Consequence
DCHS1
NM_003737.4 3_prime_UTR
NM_003737.4 3_prime_UTR
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.633
Genes affected
DCHS1 (HGNC:13681): (dachsous cadherin-related 1) This gene is a member of the cadherin superfamily whose members encode calcium-dependent cell-cell adhesion molecules. The encoded protein has a signal peptide, 27 cadherin repeat domains and a unique cytoplasmic region. This particular cadherin family member is expressed in fibroblasts but not in melanocytes or keratinocytes. The cell-cell adhesion of fibroblasts is thought to be necessary for wound healing. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -20 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.81).
BP6
Variant 11-6621604-C-T is Benign according to our data. Variant chr11-6621604-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 1194107.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BS1
Variant frequency is greater than expected in population sas. gnomad4 allele frequency = 0.0103 (1564/152320) while in subpopulation SAS AF= 0.0512 (247/4828). AF 95% confidence interval is 0.0459. There are 13 homozygotes in gnomad4. There are 800 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
High Homozygotes in GnomAd4 at 13 AD,AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DCHS1 | NM_003737.4 | c.*175G>A | 3_prime_UTR_variant | 21/21 | ENST00000299441.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DCHS1 | ENST00000299441.5 | c.*175G>A | 3_prime_UTR_variant | 21/21 | 1 | NM_003737.4 | P1 | ||
DCHS1-AS1 | ENST00000526456.1 | n.154C>T | non_coding_transcript_exon_variant | 1/2 | 4 |
Frequencies
GnomAD3 genomes AF: 0.0103 AC: 1563AN: 152202Hom.: 13 Cov.: 32
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GnomAD3 exomes AF: 0.0130 AC: 1769AN: 135998Hom.: 28 AF XY: 0.0153 AC XY: 1126AN XY: 73770
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GnomAD4 exome AF: 0.0114 AC: 7009AN: 614414Hom.: 121 Cov.: 8 AF XY: 0.0133 AC XY: 4358AN XY: 328436
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GnomAD4 genome AF: 0.0103 AC: 1564AN: 152320Hom.: 13 Cov.: 32 AF XY: 0.0107 AC XY: 800AN XY: 74484
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ClinVar
Significance: Likely benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:2
Likely benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Apr 14, 2019 | - - |
Computational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at