rs201105747
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_001846.4(COL4A2):c.5068G>A(p.Ala1690Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00046 in 1,613,472 control chromosomes in the GnomAD database, including 4 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_001846.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
COL4A2 | NM_001846.4 | c.5068G>A | p.Ala1690Thr | missense_variant | Exon 48 of 48 | ENST00000360467.7 | NP_001837.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
COL4A2 | ENST00000360467.7 | c.5068G>A | p.Ala1690Thr | missense_variant | Exon 48 of 48 | 5 | NM_001846.4 | ENSP00000353654.5 | ||
COL4A2 | ENST00000463084.1 | n.666G>A | non_coding_transcript_exon_variant | Exon 3 of 3 | 3 | |||||
COL4A2 | ENST00000648222.1 | n.756G>A | non_coding_transcript_exon_variant | Exon 1 of 1 | ||||||
COL4A2 | ENST00000650225.1 | n.2723G>A | non_coding_transcript_exon_variant | Exon 19 of 19 |
Frequencies
GnomAD3 genomes AF: 0.00141 AC: 215AN: 152196Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000490 AC: 122AN: 248884Hom.: 0 AF XY: 0.000362 AC XY: 49AN XY: 135258
GnomAD4 exome AF: 0.000361 AC: 528AN: 1461160Hom.: 4 Cov.: 34 AF XY: 0.000345 AC XY: 251AN XY: 726894
GnomAD4 genome AF: 0.00141 AC: 215AN: 152312Hom.: 0 Cov.: 33 AF XY: 0.00130 AC XY: 97AN XY: 74488
ClinVar
Submissions by phenotype
Porencephaly 2 Benign:2
This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). Publications were found based on this search. The evidence from the literature, in combination with allele frequency data from public databases where available, was sufficient to determine this variant is unlikely to cause disease. Therefore, this variant is classified as likely benign. -
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not provided Benign:2
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COL4A2: BS1, BS2 -
COL4A2-related disorder Benign:1
This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -
Hemorrhage, intracerebral, susceptibility to Other:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at