rs1147990
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_004623.5(TTC4):c.139T>A(p.Ser47Thr) variant causes a missense change. The variant allele was found at a frequency of 0.545 in 1,611,986 control chromosomes in the GnomAD database, including 247,383 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/20 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.
Frequency
Consequence
NM_004623.5 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 |
---|---|---|---|---|---|---|---|
TTC4 | NM_004623.5 | c.139T>A | p.Ser47Thr | missense_variant | 2/10 | ENST00000371281.4 | |
MROH7-TTC4 | NR_037639.2 | n.4317T>A | non_coding_transcript_exon_variant | 25/33 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TTC4 | ENST00000371281.4 | c.139T>A | p.Ser47Thr | missense_variant | 2/10 | 1 | NM_004623.5 | P1 | |
TTC4 | ENST00000371284.9 | n.305T>A | non_coding_transcript_exon_variant | 2/10 | 5 | ||||
TTC4 | ENST00000486621.1 | n.183T>A | non_coding_transcript_exon_variant | 2/3 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.552 AC: 83895AN: 151904Hom.: 23914 Cov.: 32
GnomAD3 exomes AF: 0.596 AC: 149236AN: 250576Hom.: 46647 AF XY: 0.597 AC XY: 80933AN XY: 135472
GnomAD4 exome AF: 0.545 AC: 795131AN: 1459964Hom.: 223452 Cov.: 39 AF XY: 0.550 AC XY: 399290AN XY: 726326
GnomAD4 genome ? AF: 0.552 AC: 83957AN: 152022Hom.: 23931 Cov.: 32 AF XY: 0.557 AC XY: 41372AN XY: 74312
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at