6-42228452-C-T
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_001395490.1(TRERF1):c.3532G>A(p.Val1178Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000378 in 1,614,066 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001395490.1 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TRERF1 | NM_001395490.1 | c.3532G>A | p.Val1178Ile | missense_variant | 18/18 | ENST00000695948.1 | |
LOC105375061 | XR_001744122.2 | n.121+3593C>T | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TRERF1 | ENST00000695948.1 | c.3532G>A | p.Val1178Ile | missense_variant | 18/18 | NM_001395490.1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000788 AC: 12AN: 152202Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000199 AC: 5AN: 251446Hom.: 0 AF XY: 0.0000147 AC XY: 2AN XY: 135904
GnomAD4 exome AF: 0.0000335 AC: 49AN: 1461864Hom.: 0 Cov.: 31 AF XY: 0.0000358 AC XY: 26AN XY: 727232
GnomAD4 genome ? AF: 0.0000788 AC: 12AN: 152202Hom.: 0 Cov.: 32 AF XY: 0.000108 AC XY: 8AN XY: 74340
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 06, 2021 | The c.3496G>A (p.V1166I) alteration is located in exon 18 (coding exon 14) of the TRERF1 gene. This alteration results from a G to A substitution at nucleotide position 3496, causing the valine (V) at amino acid position 1166 to be replaced by an isoleucine (I). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at