rs1866389
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_003248.6(THBS4):āc.1159G>Cā(p.Ala387Pro) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.207 in 1,612,566 control chromosomes in the GnomAD database, including 36,494 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. A387V) has been classified as Uncertain significance.
Frequency
Consequence
NM_003248.6 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -12 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
THBS4 | NM_003248.6 | c.1159G>C | p.Ala387Pro | missense_variant | 9/22 | ENST00000350881.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
THBS4 | ENST00000350881.6 | c.1159G>C | p.Ala387Pro | missense_variant | 9/22 | 1 | NM_003248.6 | P1 | |
THBS4-AS1 | ENST00000503007.5 | n.428+3072C>G | intron_variant, non_coding_transcript_variant | 3 | |||||
THBS4 | ENST00000511733.1 | c.886G>C | p.Ala296Pro | missense_variant | 9/22 | 2 | |||
THBS4-AS1 | ENST00000661210.1 | n.2794C>G | non_coding_transcript_exon_variant | 3/3 |
Frequencies
GnomAD3 genomes ? AF: 0.171 AC: 25955AN: 152094Hom.: 2508 Cov.: 32
GnomAD3 exomes AF: 0.173 AC: 43428AN: 250482Hom.: 4352 AF XY: 0.180 AC XY: 24364AN XY: 135426
GnomAD4 exome AF: 0.210 AC: 307178AN: 1460354Hom.: 33981 Cov.: 32 AF XY: 0.210 AC XY: 152425AN XY: 726552
GnomAD4 genome ? AF: 0.171 AC: 25971AN: 152212Hom.: 2513 Cov.: 32 AF XY: 0.167 AC XY: 12423AN XY: 74424
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at