chr2-189010695-T-G
Variant summary
Our verdict is Benign. Variant got -19 ACMG points: 1P and 20B. PP2BP4_StrongBP6_Very_StrongBA1
The NM_000090.4(COL3A1):c.4059T>G(p.His1353Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.999 in 1,614,158 control chromosomes in the GnomAD database, including 805,640 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_000090.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -19 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
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COL3A1 | ENST00000304636.9 | c.4059T>G | p.His1353Gln | missense_variant | Exon 50 of 51 | 1 | NM_000090.4 | ENSP00000304408.4 | ||
COL3A1 | ENST00000450867.2 | c.3960T>G | p.His1320Gln | missense_variant | Exon 49 of 50 | 1 | ENSP00000415346.2 | |||
COL3A1 | ENST00000487010.1 | n.1438T>G | non_coding_transcript_exon_variant | Exon 2 of 3 | 2 |
Frequencies
GnomAD3 genomes AF: 0.996 AC: 151524AN: 152196Hom.: 75430 Cov.: 32
GnomAD3 exomes AF: 0.999 AC: 250991AN: 251310Hom.: 125341 AF XY: 0.999 AC XY: 135669AN XY: 135802
GnomAD4 exome AF: 0.999 AC: 1461064AN: 1461844Hom.: 730152 Cov.: 54 AF XY: 1.00 AC XY: 726861AN XY: 727222
GnomAD4 genome AF: 0.996 AC: 151641AN: 152314Hom.: 75488 Cov.: 32 AF XY: 0.996 AC XY: 74169AN XY: 74472
ClinVar
Submissions by phenotype
not specified Benign:4
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This is a RefSeq error. The reference base (c.4059T) is the minor allele. This a llele (T) has been identified in 1.5% (66/4406) of African American chromosomes by the NHLBI Exome Sequencing Project (http://evs.gs.washington.edu/EVS/; dbSNP rs1516446) and thus meets criteria to be classified as benign. -
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Ehlers-Danlos syndrome, type 4 Benign:4
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Familial thoracic aortic aneurysm and aortic dissection Benign:2
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not provided Benign:2
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Polymicrogyria with or without vascular-type Ehlers-Danlos syndrome Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at