11-125677980-G-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001612.6(ACRV1):c.370C>T(p.Leu124Phe) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000226 in 1,460,276 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001612.6 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 |
---|---|---|---|---|---|---|---|
ACRV1 | NM_001612.6 | c.370C>T | p.Leu124Phe | missense_variant | 2/4 | ENST00000533904.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ACRV1 | ENST00000533904.6 | c.370C>T | p.Leu124Phe | missense_variant | 2/4 | 1 | NM_001612.6 | A2 | |
ACRV1 | ENST00000315608.7 | c.370C>T | p.Leu124Phe | missense_variant | 2/4 | 1 | P2 | ||
ACRV1 | ENST00000530048.5 | c.205C>T | p.Leu69Phe | missense_variant | 3/5 | 3 | A2 | ||
ACRV1 | ENST00000527795.1 | c.160C>T | p.Leu54Phe | missense_variant | 3/5 | 2 | A2 |
Frequencies
GnomAD3 genomes Cov.: 31
GnomAD3 exomes AF: 0.00000398 AC: 1AN: 251408Hom.: 0 AF XY: 0.00000736 AC XY: 1AN XY: 135870
GnomAD4 exome AF: 0.0000226 AC: 33AN: 1460276Hom.: 0 Cov.: 32 AF XY: 0.0000234 AC XY: 17AN XY: 726390
GnomAD4 genome Cov.: 31
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Nov 01, 2022 | The c.370C>T (p.L124F) alteration is located in exon 2 (coding exon 2) of the ACRV1 gene. This alteration results from a C to T substitution at nucleotide position 370, causing the leucine (L) at amino acid position 124 to be replaced by a phenylalanine (F). 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