chr11-6621526-TGAG-T
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBS1BS2
The NM_003737.4(DCHS1):c.*250_*252del variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00268 in 631,526 control chromosomes in the GnomAD database, including 35 homozygotes. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.0075 ( 20 hom., cov: 32)
Exomes 𝑓: 0.0011 ( 15 hom. )
Consequence
DCHS1
NM_003737.4 3_prime_UTR
NM_003737.4 3_prime_UTR
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 0.539
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]
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -10 ACMG points.
BP6
?
Variant 11-6621526-TGAG-T is Benign according to our data. Variant chr11-6621526-TGAG-T is described in ClinVar as [Likely_benign]. Clinvar id is 1203506.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
?
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.00751 (1143/152256) while in subpopulation AFR AF= 0.026 (1082/41542). AF 95% confidence interval is 0.0248. There are 20 homozygotes in gnomad4. There are 550 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAd at 20 AD,AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DCHS1 | NM_003737.4 | c.*250_*252del | 3_prime_UTR_variant | 21/21 | ENST00000299441.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DCHS1 | ENST00000299441.5 | c.*250_*252del | 3_prime_UTR_variant | 21/21 | 1 | NM_003737.4 | P1 | ||
DCHS1-AS1 | ENST00000526456.1 | n.80_82del | non_coding_transcript_exon_variant | 1/2 | 4 |
Frequencies
GnomAD3 genomes ? AF: 0.00751 AC: 1143AN: 152138Hom.: 20 Cov.: 32
GnomAD3 genomes
?
AF:
AC:
1143
AN:
152138
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: 0.00198 AC: 229AN: 115714Hom.: 3 AF XY: 0.00158 AC XY: 98AN XY: 61894
GnomAD3 exomes
AF:
AC:
229
AN:
115714
Hom.:
AF XY:
AC XY:
98
AN XY:
61894
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: 0.00115 AC: 551AN: 479270Hom.: 15 AF XY: 0.000930 AC XY: 239AN XY: 257082
GnomAD4 exome
AF:
AC:
551
AN:
479270
Hom.:
AF XY:
AC XY:
239
AN XY:
257082
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: 0.00751 AC: 1143AN: 152256Hom.: 20 Cov.: 32 AF XY: 0.00739 AC XY: 550AN XY: 74460
GnomAD4 genome
?
AF:
AC:
1143
AN:
152256
Hom.:
Cov.:
32
AF XY:
AC XY:
550
AN XY:
74460
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:
6
AN:
3478
ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Oct 09, 2018 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
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