6-49606843-A-G
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_000324.3(RHAG):c.1212+5T>C variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000708 in 1,581,584 control chromosomes in the GnomAD database, including 3 homozygotes. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_000324.3 splice_region, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
RHAG | ENST00000371175.10 | c.1212+5T>C | splice_region_variant, intron_variant | Intron 9 of 9 | 1 | NM_000324.3 | ENSP00000360217.4 | |||
RHAG | ENST00000646272.1 | c.1217T>C | p.Leu406Pro | missense_variant | Exon 9 of 10 | ENSP00000494337.1 | ||||
RHAG | ENST00000646963.1 | c.1138+307T>C | intron_variant | Intron 8 of 8 | ENSP00000495337.1 | |||||
RHAG | ENST00000646939.1 | c.*34+5T>C | splice_region_variant, intron_variant | Intron 8 of 8 | ENSP00000494709.1 |
Frequencies
GnomAD3 genomes AF: 0.00104 AC: 158AN: 152194Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.00104 AC: 261AN: 250582Hom.: 1 AF XY: 0.000989 AC XY: 134AN XY: 135422
GnomAD4 exome AF: 0.000672 AC: 961AN: 1429390Hom.: 3 Cov.: 27 AF XY: 0.000679 AC XY: 484AN XY: 713264
GnomAD4 genome AF: 0.00104 AC: 158AN: 152194Hom.: 0 Cov.: 33 AF XY: 0.00135 AC XY: 100AN XY: 74346
ClinVar
Submissions by phenotype
not provided Benign:2
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Jun 01, 2024 | RHAG: BP4, BS2 - |
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jan 14, 2025 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at