2-10122775-G-T
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The ENST00000360566.6(RRM2):c.157G>T(p.Ala53Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000631 in 1,568,404 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/18 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
ENST00000360566.6 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RRM2 | NM_001034.4 | c.-24G>T | 5_prime_UTR_variant | 1/10 | ENST00000304567.10 | ||
RRM2 | NM_001165931.1 | c.157G>T | p.Ala53Ser | missense_variant | 1/10 | ||
RRM2 | NR_164157.1 | n.37G>T | non_coding_transcript_exon_variant | 1/13 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RRM2 | ENST00000304567.10 | c.-24G>T | 5_prime_UTR_variant | 1/10 | 1 | NM_001034.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000723 AC: 11AN: 152184Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000131 AC: 23AN: 175562Hom.: 0 AF XY: 0.0000956 AC XY: 9AN XY: 94182
GnomAD4 exome AF: 0.0000621 AC: 88AN: 1416102Hom.: 0 Cov.: 30 AF XY: 0.0000500 AC XY: 35AN XY: 700146
GnomAD4 genome ? AF: 0.0000722 AC: 11AN: 152302Hom.: 0 Cov.: 32 AF XY: 0.0000940 AC XY: 7AN XY: 74484
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jun 02, 2023 | The c.157G>T (p.A53S) alteration is located in exon 1 (coding exon 1) of the RRM2 gene. This alteration results from a G to T substitution at nucleotide position 157, causing the alanine (A) at amino acid position 53 to be replaced by a serine (S). 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