NM_001846.4:c.1596+101G>T

Variant names:

• chr13-110459035-G-T
• rs4773186
• NM_001846.4:c.1596+101G>T

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_001846.4(COL4A2):​c.1596+101G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: not found (cov: 32)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: COL4A2 NM_001846.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0100
• Publications: 7 publications found

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-AS2 (HGNC:39849): (COL4A2 antisense RNA 2)

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001846.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	COL4A2	NM_001846.4	MANE Select	c.1596+101G>T		intron	N/A	NP_001837.2
	COL4A2-AS2	NR_171022.1		n.266-749C>A		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	COL4A2	ENST00000360467.7	TSL:5 MANE Select	c.1596+101G>T		intron	N/A	ENSP00000353654.5
	COL4A2	ENST00000617564.3	TSL:6	c.*20G>T		3_prime_UTR	Exon 22 of 22	ENSP00000481492.3
	COL4A2	ENST00000714399.1		c.1677+101G>T		intron	N/A	ENSP00000519666.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 1060500 Hom.: 0 Cov.: 14 AF XY: 0.00 AC XY: 0 AN XY: 521300

African (AFR) AF: 0.00 AC: 0 AN: 22348

American (AMR) AF: 0.00 AC: 0 AN: 17282

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 17050

East Asian (EAS) AF: 0.00 AC: 0 AN: 31884

South Asian (SAS) AF: 0.00 AC: 0 AN: 56028

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 42018

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 3090

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 825300

Other (OTH) AF: 0.00 AC: 0 AN: 45500

GnomAD4 genome Cov.: 32

Alfa AF: 0.00 Hom.: 55265

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.41
DANN	Benign	0.51
PhyloP100		-0.010

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

Other links and lift over

dbSNP: rs4773186; hg19: chr13-111111382;