5-175492180-A-G
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_022754.7(SFXN1):āc.77A>Gā(p.Asn26Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00103 in 1,614,124 control chromosomes in the GnomAD database, including 11 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_022754.7 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SFXN1 | NM_022754.7 | c.77A>G | p.Asn26Ser | missense_variant | 2/11 | ENST00000321442.10 | NP_073591.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SFXN1 | ENST00000321442.10 | c.77A>G | p.Asn26Ser | missense_variant | 2/11 | 1 | NM_022754.7 | ENSP00000316905.5 |
Frequencies
GnomAD3 genomes AF: 0.00530 AC: 807AN: 152208Hom.: 8 Cov.: 33
GnomAD3 exomes AF: 0.00147 AC: 369AN: 251370Hom.: 2 AF XY: 0.00103 AC XY: 140AN XY: 135868
GnomAD4 exome AF: 0.000583 AC: 852AN: 1461798Hom.: 3 Cov.: 31 AF XY: 0.000494 AC XY: 359AN XY: 727194
GnomAD4 genome AF: 0.00530 AC: 808AN: 152326Hom.: 8 Cov.: 33 AF XY: 0.00490 AC XY: 365AN XY: 74480
ClinVar
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Mar 29, 2018 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at