chr6-169222396-G-A
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 1P and 10B. PP2BP4_StrongBP6_ModerateBS2
The NM_003247.5(THBS2):c.3074C>T(p.Ala1025Val) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000218 in 1,613,742 control chromosomes in the GnomAD database, including 5 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★). Synonymous variant affecting the same amino acid position (i.e. A1025A) has been classified as Benign.
Frequency
Consequence
NM_003247.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -9 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
THBS2 | NM_003247.5 | c.3074C>T | p.Ala1025Val | missense_variant | 19/22 | ENST00000617924.6 | |
THBS2-AS1 | NR_134621.1 | n.681+7909G>A | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
THBS2 | ENST00000617924.6 | c.3074C>T | p.Ala1025Val | missense_variant | 19/22 | 1 | NM_003247.5 | P4 | |
THBS2-AS1 | ENST00000660724.1 | n.639+7909G>A | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes ? AF: 0.000335 AC: 51AN: 152226Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000848 AC: 213AN: 251324Hom.: 4 AF XY: 0.000647 AC XY: 88AN XY: 135910
GnomAD4 exome AF: 0.000205 AC: 300AN: 1461398Hom.: 5 Cov.: 34 AF XY: 0.000186 AC XY: 135AN XY: 727008
GnomAD4 genome ? AF: 0.000335 AC: 51AN: 152344Hom.: 0 Cov.: 33 AF XY: 0.000416 AC XY: 31AN XY: 74500
ClinVar
Submissions by phenotype
THBS2-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | May 24, 2019 | This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at