20-48921863-G-A
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_006420.3(ARFGEF2):c.-27G>A variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000634 in 1,508,868 control chromosomes in the GnomAD database, including 5 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_006420.3 5_prime_UTR
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ARFGEF2 | NM_006420.3 | c.-27G>A | 5_prime_UTR_variant | Exon 1 of 39 | ENST00000371917.5 | NP_006411.2 | ||
ARFGEF2 | NM_001410846.1 | c.-27G>A | 5_prime_UTR_variant | Exon 1 of 39 | NP_001397775.1 | |||
ARFGEF2 | XM_047439832.1 | c.-436G>A | 5_prime_UTR_variant | Exon 1 of 37 | XP_047295788.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000515 AC: 78AN: 151512Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00155 AC: 188AN: 121670Hom.: 3 AF XY: 0.00186 AC XY: 122AN XY: 65650
GnomAD4 exome AF: 0.000648 AC: 879AN: 1357246Hom.: 5 Cov.: 31 AF XY: 0.000804 AC XY: 538AN XY: 669174
GnomAD4 genome AF: 0.000514 AC: 78AN: 151622Hom.: 0 Cov.: 32 AF XY: 0.000432 AC XY: 32AN XY: 74152
ClinVar
Submissions by phenotype
not specified Benign:1
This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -
not provided Benign:1
- -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at