chr13-110203806-A-C

Position:

• chr13-110203806-A-C

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The NM_001845.6(COL4A1):​c.958-199T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.573 in 152,030 control chromosomes in the GnomAD database, including 25,982 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.57 (25982 hom., cov: 33)
• Consequence: COL4A1 NM_001845.6 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.597

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]

ACMG classification

Verdict is Benign. Variant got -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BP6: Variant 13-110203806-A-C is Benign according to our data. Variant chr13-110203806-A-C is described in ClinVar as [Benign]. Clinvar id is 1293046.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.742 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
COL4A1	NM_001845.6	c.958-199T>G		intron_variant		ENST00000375820.10	NP_001836.3
COL4A1	NM_001303110.2	c.958-199T>G		intron_variant			NP_001290039.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
COL4A1	ENST00000375820.10	c.958-199T>G		intron_variant		1	NM_001845.6	ENSP00000364979	P1
COL4A1	ENST00000543140.6	c.958-199T>G		intron_variant		1		ENSP00000443348
COL4A1	ENST00000647797.1	c.837-199T>G		intron_variant				ENSP00000497756
COL4A1	ENST00000649738.1	n.1088-199T>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.574 AC: 87164 AN: 151912 Hom.: 25986 Cov.: 33

Gnomad AFR AF: 0.413

Gnomad AMI AF: 0.879

Gnomad AMR AF: 0.543

Gnomad ASJ AF: 0.698

Gnomad EAS AF: 0.763

Gnomad SAS AF: 0.699

Gnomad FIN AF: 0.609

Gnomad MID AF: 0.639

Gnomad NFE AF: 0.638

Gnomad OTH AF: 0.619

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.573 AC: 87174 AN: 152030 Hom.: 25982 Cov.: 33 AF XY: 0.575 AC XY: 42749 AN XY: 74314

Gnomad4 AFR AF: 0.412

Gnomad4 AMR AF: 0.543

Gnomad4 ASJ AF: 0.698

Gnomad4 EAS AF: 0.762

Gnomad4 SAS AF: 0.700

Gnomad4 FIN AF: 0.609

Gnomad4 NFE AF: 0.638

Gnomad4 OTH AF: 0.616

Alfa AF: 0.621 Hom.: 12710

Bravo AF: 0.562

Asia WGS AF: 0.684 AC: 2379 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Jun 26, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	1.6
DANN	Benign	0.49

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs648705; hg19: chr13-110856153; COSMIC: COSV65421097; COSMIC: COSV65421097;