chr13-110465755-G-A

Position:

• chr13-110465755-G-A

Variant summary

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

The NM_001846.4(COL4A2):​c.1978+149G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.563 in 862,410 control chromosomes in the GnomAD database, including 141,431 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.57 (25158 hom., cov: 33)
  • Exomes 𝑓: 0.56 (116273 hom.)
• Consequence: COL4A2 NM_001846.4 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.665

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]

ACMG classification

Verdict is Benign. Variant got -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BP6: Variant 13-110465755-G-A is Benign according to our data. Variant chr13-110465755-G-A is described in ClinVar as [Benign]. Clinvar id is 1238517.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.608 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
COL4A2	NM_001846.4	c.1978+149G>A		intron_variant		ENST00000360467.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
COL4A2	ENST00000360467.7	c.1978+149G>A		intron_variant		5	NM_001846.4	P1

Frequencies

GnomAD3 genomes AF: 0.568 AC: 86297 AN: 151978 Hom.: 25142 Cov.: 33

Gnomad AFR AF: 0.615

Gnomad AMI AF: 0.675

Gnomad AMR AF: 0.494

Gnomad ASJ AF: 0.668

Gnomad EAS AF: 0.281

Gnomad SAS AF: 0.459

Gnomad FIN AF: 0.429

Gnomad MID AF: 0.731

Gnomad NFE AF: 0.599

Gnomad OTH AF: 0.581

GnomAD4 exome AF: 0.562 AC: 399152 AN: 710314 Hom.: 116273 AF XY: 0.560 AC XY: 201854 AN XY: 360748

Gnomad4 AFR exome AF: 0.618

Gnomad4 AMR exome AF: 0.445

Gnomad4 ASJ exome AF: 0.646

Gnomad4 EAS exome AF: 0.242

Gnomad4 SAS exome AF: 0.472

Gnomad4 FIN exome AF: 0.442

Gnomad4 NFE exome AF: 0.600

Gnomad4 OTH exome AF: 0.570

GnomAD4 genome AF: 0.568 AC: 86368 AN: 152096 Hom.: 25158 Cov.: 33 AF XY: 0.556 AC XY: 41342 AN XY: 74352

Gnomad4 AFR AF: 0.615

Gnomad4 AMR AF: 0.494

Gnomad4 ASJ AF: 0.668

Gnomad4 EAS AF: 0.282

Gnomad4 SAS AF: 0.460

Gnomad4 FIN AF: 0.429

Gnomad4 NFE AF: 0.599

Gnomad4 OTH AF: 0.581

Alfa AF: 0.593 Hom.: 32625

Bravo AF: 0.574

Asia WGS AF: 0.392 AC: 1364 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 29, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.5
DANN	Benign	0.37

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: rs1983931; hg19: chr13-111118102;