chr17-1635080-A-C
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_003693.4(SCARF1):āc.2171T>Gā(p.Val724Gly) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000682 in 1,613,648 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. V724F) has been classified as Uncertain significance.
Frequency
Consequence
NM_003693.4 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 |
---|---|---|---|---|---|---|---|
SCARF1 | NM_003693.4 | c.2171T>G | p.Val724Gly | missense_variant | 11/11 | ENST00000263071.9 | |
SCARF1 | NM_145350.3 | c.*424T>G | 3_prime_UTR_variant | 11/11 | |||
SCARF1 | NR_028075.3 | n.2136T>G | non_coding_transcript_exon_variant | 11/11 | |||
SCARF1 | NR_102409.2 | n.2243T>G | non_coding_transcript_exon_variant | 11/11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SCARF1 | ENST00000263071.9 | c.2171T>G | p.Val724Gly | missense_variant | 11/11 | 1 | NM_003693.4 | P2 |
Frequencies
GnomAD3 genomes AF: 0.00000658 AC: 1AN: 152034Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.00000400 AC: 1AN: 249934Hom.: 0 AF XY: 0.00000739 AC XY: 1AN XY: 135362
GnomAD4 exome AF: 0.00000684 AC: 10AN: 1461614Hom.: 0 Cov.: 30 AF XY: 0.00000688 AC XY: 5AN XY: 727098
GnomAD4 genome AF: 0.00000658 AC: 1AN: 152034Hom.: 0 Cov.: 33 AF XY: 0.0000135 AC XY: 1AN XY: 74272
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 01, 2024 | The c.2171T>G (p.V724G) alteration is located in exon 11 (coding exon 11) of the SCARF1 gene. This alteration results from a T to G substitution at nucleotide position 2171, causing the valine (V) at amino acid position 724 to be replaced by a glycine (G). 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