rs598819
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Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_001845.6(COL4A1):c.780+60T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.996 in 1,443,548 control chromosomes in the GnomAD database, including 716,581 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.98 ( 73396 hom., cov: 30)
Exomes 𝑓: 1.0 ( 643185 hom. )
Consequence
COL4A1
NM_001845.6 intron
NM_001845.6 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.854
Genes affected
COL4A1 (HGNC:2202): (collagen type IV alpha 1 chain) This gene encodes a type IV collagen alpha protein. Type IV collagen proteins are integral components of basement membranes. This gene shares a bidirectional promoter with a paralogous gene on the opposite strand. The protein consists of an amino-terminal 7S domain, a triple-helix forming collagenous domain, and a carboxy-terminal non-collagenous domain. It functions as part of a heterotrimer and interacts with other extracellular matrix components such as perlecans, proteoglycans, and laminins. In addition, proteolytic cleavage of the non-collagenous carboxy-terminal domain results in a biologically active fragment known as arresten, which has anti-angiogenic and tumor suppressor properties. Mutations in this gene cause porencephaly, cerebrovascular disease, and renal and muscular defects. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Dec 2014]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -14 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.88).
BP6
?
Variant 13-110207343-A-G is Benign according to our data. Variant chr13-110207343-A-G is described in ClinVar as [Benign]. Clinvar id is 1235813.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.994 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
COL4A1 | NM_001845.6 | c.780+60T>C | intron_variant | ENST00000375820.10 | |||
COL4A1 | NM_001303110.2 | c.780+60T>C | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
COL4A1 | ENST00000375820.10 | c.780+60T>C | intron_variant | 1 | NM_001845.6 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.981 AC: 149310AN: 152132Hom.: 73356 Cov.: 30
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GnomAD4 exome AF: 0.998 AC: 1288759AN: 1291298Hom.: 643185 AF XY: 0.998 AC XY: 650422AN XY: 651496
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GnomAD4 genome ? AF: 0.981 AC: 149405AN: 152250Hom.: 73396 Cov.: 30 AF XY: 0.982 AC XY: 73122AN XY: 74440
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jun 26, 2018 | - - |
Computational scores
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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