rs7327528

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_001846.4(COL4A2):​c.-44-163G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0627 in 152,176 control chromosomes in the GnomAD database, including 320 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.063 ( 320 hom., cov: 32)

Consequence

COL4A2
NM_001846.4 intron

Scores

2

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: 0.790
Variant links:
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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.85).
BP6
Variant 13-110307697-G-C is Benign according to our data. Variant chr13-110307697-G-C is described in ClinVar as [Benign]. Clinvar id is 1272966.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0644 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
COL4A2NM_001846.4 linkuse as main transcriptc.-44-163G>C intron_variant ENST00000360467.7 NP_001837.2 P08572A0A024RDW8

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
COL4A2ENST00000360467.7 linkuse as main transcriptc.-44-163G>C intron_variant 5 NM_001846.4 ENSP00000353654.5 P08572

Frequencies

GnomAD3 genomes
AF:
0.0627
AC:
9528
AN:
152058
Hom.:
317
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0636
Gnomad AMI
AF:
0.122
Gnomad AMR
AF:
0.0536
Gnomad ASJ
AF:
0.0761
Gnomad EAS
AF:
0.0272
Gnomad SAS
AF:
0.0552
Gnomad FIN
AF:
0.0595
Gnomad MID
AF:
0.0791
Gnomad NFE
AF:
0.0660
Gnomad OTH
AF:
0.0713
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.0627
AC:
9544
AN:
152176
Hom.:
320
Cov.:
32
AF XY:
0.0629
AC XY:
4681
AN XY:
74414
show subpopulations
Gnomad4 AFR
AF:
0.0639
Gnomad4 AMR
AF:
0.0535
Gnomad4 ASJ
AF:
0.0761
Gnomad4 EAS
AF:
0.0275
Gnomad4 SAS
AF:
0.0546
Gnomad4 FIN
AF:
0.0595
Gnomad4 NFE
AF:
0.0660
Gnomad4 OTH
AF:
0.0701
Alfa
AF:
0.0650
Hom.:
38
Bravo
AF:
0.0617
Asia WGS
AF:
0.0480
AC:
168
AN:
3478

ClinVar

Significance: Benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link

Submissions by phenotype

not provided Benign:2
Benign, criteria provided, single submitternot providedBreakthrough Genomics, Breakthrough Genomics-- -
Benign, criteria provided, single submitterclinical testingGeneDxJun 29, 2018- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.85
CADD
Benign
6.4
DANN
Benign
0.42

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.010
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

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs7327528; hg19: chr13-110960044; API