chr17-1635362-C-T
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_003693.4(SCARF1):c.1889G>A(p.Arg630Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000211 in 1,613,094 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_003693.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SCARF1 | NM_003693.4 | c.1889G>A | p.Arg630Gln | missense_variant | 11/11 | ENST00000263071.9 | |
SCARF1 | NM_145350.3 | c.*142G>A | 3_prime_UTR_variant | 11/11 | |||
SCARF1 | NR_028075.3 | n.1854G>A | non_coding_transcript_exon_variant | 11/11 | |||
SCARF1 | NR_102409.2 | n.1961G>A | non_coding_transcript_exon_variant | 11/11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SCARF1 | ENST00000263071.9 | c.1889G>A | p.Arg630Gln | missense_variant | 11/11 | 1 | NM_003693.4 | P2 |
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152208Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000201 AC: 5AN: 248816Hom.: 0 AF XY: 0.0000148 AC XY: 2AN XY: 134884
GnomAD4 exome AF: 0.0000219 AC: 32AN: 1460768Hom.: 0 Cov.: 37 AF XY: 0.0000206 AC XY: 15AN XY: 726598
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152326Hom.: 0 Cov.: 33 AF XY: 0.0000134 AC XY: 1AN XY: 74478
ClinVar
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 03, 2022 | This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at