7-150372331-C-G
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_001099695.2(REPIN1):āc.1261C>Gā(p.Pro421Ala) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000592 in 1,521,014 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 (ā ).
Frequency
Consequence
NM_001099695.2 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 |
---|---|---|---|---|---|---|---|
REPIN1 | NM_001099695.2 | c.1261C>G | p.Pro421Ala | missense_variant | 3/3 | ENST00000489432.7 | |
REPIN1-AS1 | NR_183429.1 | n.103+510G>C | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
REPIN1 | ENST00000489432.7 | c.1261C>G | p.Pro421Ala | missense_variant | 3/3 | 2 | NM_001099695.2 | P4 | |
REPIN1-AS1 | ENST00000488310.1 | n.98+162G>C | intron_variant, non_coding_transcript_variant | 4 |
Frequencies
GnomAD3 genomes AF: 0.0000263 AC: 4AN: 152088Hom.: 0 Cov.: 33
GnomAD4 exome AF: 0.00000365 AC: 5AN: 1368816Hom.: 0 Cov.: 32 AF XY: 0.00000296 AC XY: 2AN XY: 675736
GnomAD4 genome AF: 0.0000263 AC: 4AN: 152198Hom.: 0 Cov.: 33 AF XY: 0.0000134 AC XY: 1AN XY: 74414
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 19, 2021 | The c.1261C>G (p.P421A) alteration is located in exon 3 (coding exon 2) of the REPIN1 gene. This alteration results from a C to G substitution at nucleotide position 1261, causing the proline (P) at amino acid position 421 to be replaced by an alanine (A). 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