6-47005872-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_153840.4(ADGRF1):c.2537G>A(p.Arg846Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000869 in 1,610,288 control chromosomes in the GnomAD database, with no homozygous occurrence. 12/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R846L) has been classified as Uncertain significance.
Frequency
Consequence
NM_153840.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ADGRF1 | ENST00000371253.7 | c.2537G>A | p.Arg846Gln | missense_variant | Exon 13 of 15 | 1 | NM_153840.4 | ENSP00000360299.2 | ||
ADGRF1 | ENST00000283297.5 | c.1946G>A | p.Arg649Gln | missense_variant | Exon 7 of 9 | 1 | ENSP00000283297.5 | |||
ADGRF1 | ENST00000449332.6 | n.2508G>A | non_coding_transcript_exon_variant | Exon 11 of 13 | 1 | |||||
ADGRF1 | ENST00000419892.6 | n.8803G>A | non_coding_transcript_exon_variant | Exon 11 of 13 | 2 |
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 152064Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000121 AC: 3AN: 248710Hom.: 0 AF XY: 0.00000744 AC XY: 1AN XY: 134482
GnomAD4 exome AF: 0.00000754 AC: 11AN: 1458106Hom.: 0 Cov.: 28 AF XY: 0.00000414 AC XY: 3AN XY: 725414
GnomAD4 genome AF: 0.0000197 AC: 3AN: 152182Hom.: 0 Cov.: 32 AF XY: 0.0000403 AC XY: 3AN XY: 74414
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.2537G>A (p.R846Q) alteration is located in exon 13 (coding exon 12) of the ADGRF1 gene. This alteration results from a G to A substitution at nucleotide position 2537, causing the arginine (R) at amino acid position 846 to be replaced by a glutamine (Q). 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