chr17-29569048-G-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_138349.4(TP53I13):c.103G>A(p.Ala35Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000305 in 1,607,052 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_138349.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TP53I13 | NM_138349.4 | c.103G>A | p.Ala35Thr | missense_variant | 2/7 | ENST00000301057.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TP53I13 | ENST00000301057.8 | c.103G>A | p.Ala35Thr | missense_variant | 2/7 | 1 | NM_138349.4 | P1 | |
ABHD15-AS1 | ENST00000581474.1 | n.153+8349G>A | intron_variant, non_coding_transcript_variant | 5 |
Frequencies
GnomAD3 genomes AF: 0.000145 AC: 22AN: 152192Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000564 AC: 13AN: 230698Hom.: 0 AF XY: 0.0000632 AC XY: 8AN XY: 126644
GnomAD4 exome AF: 0.0000186 AC: 27AN: 1454860Hom.: 1 Cov.: 31 AF XY: 0.0000221 AC XY: 16AN XY: 723286
GnomAD4 genome AF: 0.000145 AC: 22AN: 152192Hom.: 0 Cov.: 32 AF XY: 0.000121 AC XY: 9AN XY: 74354
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 08, 2021 | The c.103G>A (p.A35T) alteration is located in exon 2 (coding exon 2) of the TP53I13 gene. This alteration results from a G to A substitution at nucleotide position 103, causing the alanine (A) at amino acid position 35 to be replaced by a threonine (T). 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