4-169116534-T-C
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_020870.4(SH3RF1):c.1874A>G(p.His625Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000174 in 1,612,824 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 (★).
Frequency
Consequence
NM_020870.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SH3RF1 | NM_020870.4 | c.1874A>G | p.His625Arg | missense_variant | 10/12 | ENST00000284637.14 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SH3RF1 | ENST00000284637.14 | c.1874A>G | p.His625Arg | missense_variant | 10/12 | 1 | NM_020870.4 | P1 | |
SH3RF1 | ENST00000508685.1 | n.1755A>G | non_coding_transcript_exon_variant | 9/9 | 1 | ||||
SH3RF1 | ENST00000511421.5 | c.*481A>G | 3_prime_UTR_variant, NMD_transcript_variant | 8/8 | 1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000723 AC: 11AN: 152200Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000282 AC: 7AN: 247930Hom.: 0 AF XY: 0.0000224 AC XY: 3AN XY: 134134
GnomAD4 exome AF: 0.0000116 AC: 17AN: 1460624Hom.: 0 Cov.: 32 AF XY: 0.00000964 AC XY: 7AN XY: 726466
GnomAD4 genome ? AF: 0.0000723 AC: 11AN: 152200Hom.: 0 Cov.: 32 AF XY: 0.0000672 AC XY: 5AN XY: 74350
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 10, 2023 | The c.1874A>G (p.H625R) alteration is located in exon 10 (coding exon 9) of the SH3RF1 gene. This alteration results from a A to G substitution at nucleotide position 1874, causing the histidine (H) at amino acid position 625 to be replaced by an arginine (R). 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