13-110211627-CAAAAT-CAAAATAAAAT

Variant names:

• chr13-110211627-C-CAAAAT
• rs3832900
• NM_001845.6:c.468+15_468+19dupATTTT

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 2P and 2B. PM2 BP6_Moderate

The NM_001845.6(COL4A1):​c.468+15_468+19dupATTTT variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000686 in 1,457,926 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Likely benign (★).

• Frequency:
  • Genomes: not found (cov: 32)
  • Exomes 𝑓: 6.9e-7 (0 hom.)
• Consequence: COL4A1 NM_001845.6 intron
• Clinical Significance: Likely benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.00300
• Publications: 0 publications found

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]

COL4A1 Gene-Disease associations (from GenCC):

• brain small vessel disease 1 with or without ocular anomalies

  Inheritance: AD Classification: DEFINITIVE, STRONG, MODERATE, SUPPORTIVE Submitted by: G2P, Ambry Genetics, PanelApp Australia, Orphanet, Genomics England PanelApp
• autosomal dominant familial hematuria-retinal arteriolar tortuosity-contractures syndrome

  Inheritance: AD Classification: STRONG, MODERATE, SUPPORTIVE Submitted by: Genomics England PanelApp, Orphanet, Ambry Genetics
• microangiopathy and leukoencephalopathy, pontine, autosomal dominant

  Inheritance: AD Classification: MODERATE Submitted by: Ambry Genetics
• familial porencephaly

  Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
• pontine autosomal dominant microangiopathy with leukoencephalopathy

  Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
• retinal arterial tortuosity

  Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
• muscular dystrophy-dystroglycanopathy, type A

  Inheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet

ACMG classification

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP6: Variant 13-110211627-C-CAAAAT is Benign according to our data. Variant chr13-110211627-C-CAAAAT is described in CliVar as Likely_benign. Clinvar id is 2162941.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr13-110211627-C-CAAAAT is described in CliVar as Likely_benign. Clinvar id is 2162941.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr13-110211627-C-CAAAAT is described in CliVar as Likely_benign. Clinvar id is 2162941.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr13-110211627-C-CAAAAT is described in CliVar as Likely_benign. Clinvar id is 2162941.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr13-110211627-C-CAAAAT is described in CliVar as Likely_benign. Clinvar id is 2162941.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr13-110211627-C-CAAAAT is described in CliVar as Likely_benign. Clinvar id is 2162941.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr13-110211627-C-CAAAAT is described in CliVar as Likely_benign. Clinvar id is 2162941.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr13-110211627-C-CAAAAT is described in CliVar as Likely_benign. Clinvar id is 2162941.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr13-110211627-C-CAAAAT is described in CliVar as Likely_benign. Clinvar id is 2162941.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr13-110211627-C-CAAAAT is described in CliVar as Likely_benign. Clinvar id is 2162941.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr13-110211627-C-CAAAAT is described in CliVar as Likely_benign. Clinvar id is 2162941.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr13-110211627-C-CAAAAT is described in CliVar as Likely_benign. Clinvar id is 2162941.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr13-110211627-C-CAAAAT is described in CliVar as Likely_benign. Clinvar id is 2162941.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr13-110211627-C-CAAAAT is described in CliVar as Likely_benign. Clinvar id is 2162941.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr13-110211627-C-CAAAAT is described in CliVar as Likely_benign. Clinvar id is 2162941.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr13-110211627-C-CAAAAT is described in CliVar as Likely_benign. Clinvar id is 2162941.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr13-110211627-C-CAAAAT is described in CliVar as Likely_benign. Clinvar id is 2162941.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr13-110211627-C-CAAAAT is described in CliVar as Likely_benign. Clinvar id is 2162941.Status of the report is criteria_provided_single_submitter, 1 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
COL4A1	NM_001845.6	c.468+15_468+19dupATTTT		intron_variant	Intron 8 of 51	ENST00000375820.10	NP_001836.3
COL4A1	NM_001303110.2	c.468+15_468+19dupATTTT		intron_variant	Intron 8 of 24		NP_001290039.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
COL4A1	ENST00000375820.10	c.468+19_468+20insATTTT		intron_variant	Intron 8 of 51	1	NM_001845.6	ENSP00000364979.4

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome AF: 6.86e-7 AC: 1 AN: 1457926 Hom.: 0 Cov.: 30 AF XY: 0.00 AC XY: 0 AN XY: 725234

African (AFR) AF: 0.00 AC: 0 AN: 33312

American (AMR) AF: 0.00 AC: 0 AN: 44092

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 26036

East Asian (EAS) AF: 0.00 AC: 0 AN: 39662

South Asian (SAS) AF: 0.00 AC: 0 AN: 85290

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 52928

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 5730

European-Non Finnish (NFE) AF: 9.00e-7 AC: 1 AN: 1110614

Other (OTH) AF: 0.00 AC: 0 AN: 60262

GnomAD4 genome Cov.: 32

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Aug 01, 2022

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Likely benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
PhyloP100		0.0030

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs3832900; hg19: chr13-110863974;