chr13-110512281-T-TA

Position:

• chr13-110512281-T-TA

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BS1 BS2

The NM_001846.4(COL4A2):​c.*102dupA variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.00053 (0 hom., cov: 0)
  • Exomes 𝑓: 0.0060 (0 hom.)
• Consequence: COL4A2 NM_001846.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.64

Genes affected

COL4A2 (HGNC:2203): (collagen type IV alpha 2 chain) This gene encodes one of the six subunits of type IV collagen, the major structural component of basement membranes. The C-terminal portion of the protein, known as canstatin, is an inhibitor of angiogenesis and tumor growth. Like the other members of the type IV collagen gene family, this gene is organized in a head-to-head conformation with another type IV collagen gene so that each gene pair shares a common promoter. [provided by RefSeq, Jul 2008]

COL4A2 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -8 ACMG points.

• BS1: Variant frequency is greater than expected in population eas. gnomad4_exome allele frequency = 0.00605 (7126/1178400) while in subpopulation EAS AF= 0.0188 (520/27722). AF 95% confidence interval is 0.0174. There are 0 homozygotes in gnomad4_exome. There are 3498 alleles in male gnomad4_exome subpopulation. Median coverage is 0. This position pass quality control queck.
• BS2: High AC in GnomAd4 at 79 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
COL4A2	NM_001846.4	c.*102dupA		3_prime_UTR_variant	48/48	ENST00000360467.7	NP_001837.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
COL4A2	ENST00000360467.7	c.*102dupA		3_prime_UTR_variant	48/48	5	NM_001846.4	ENSP00000353654.5
COL4A2	ENST00000648222.1	n.929dupA		non_coding_transcript_exon_variant	1/1
COL4A2	ENST00000650225.1	n.2896dupA		non_coding_transcript_exon_variant	19/19

Frequencies

GnomAD3 genomes AF: 0.000521 AC: 78 AN: 149648 Hom.: 0 Cov.: 0

Gnomad AFR AF: 0.00123

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000664

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.000786

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.000100

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000193

Gnomad OTH AF: 0.00

GnomAD4 exome AF: 0.00605 AC: 7126 AN: 1178400 Hom.: 0 Cov.: 0 AF XY: 0.00609 AC XY: 3498 AN XY: 574750

Gnomad4 AFR exome AF: 0.00776

Gnomad4 AMR exome AF: 0.00863

Gnomad4 ASJ exome AF: 0.00546

Gnomad4 EAS exome AF: 0.0188

Gnomad4 SAS exome AF: 0.00791

Gnomad4 FIN exome AF: 0.00631

Gnomad4 NFE exome AF: 0.00544

Gnomad4 OTH exome AF: 0.00636

GnomAD4 genome AF: 0.000528 AC: 79 AN: 149754 Hom.: 0 Cov.: 0 AF XY: 0.000521 AC XY: 38 AN XY: 73004

Gnomad4 AFR AF: 0.00125

Gnomad4 AMR AF: 0.000663

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.000789

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.000100

Gnomad4 NFE AF: 0.000193

Gnomad4 OTH AF: 0.00

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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: rs397838577; hg19: chr13-111164628;