17-1635082-C-G
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_003693.4(SCARF1):āc.2169G>Cā(p.Lys723Asn) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000613 in 1,613,888 control chromosomes in the GnomAD database, including 1 homozygotes. 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 ).
Frequency
Consequence
NM_003693.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SCARF1 | NM_003693.4 | c.2169G>C | p.Lys723Asn | missense_variant | 11/11 | ENST00000263071.9 | |
SCARF1 | NM_145350.3 | c.*422G>C | 3_prime_UTR_variant | 11/11 | |||
SCARF1 | NR_028075.3 | n.2134G>C | non_coding_transcript_exon_variant | 11/11 | |||
SCARF1 | NR_102409.2 | n.2241G>C | non_coding_transcript_exon_variant | 11/11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SCARF1 | ENST00000263071.9 | c.2169G>C | p.Lys723Asn | missense_variant | 11/11 | 1 | NM_003693.4 | P2 |
Frequencies
GnomAD3 genomes AF: 0.000355 AC: 54AN: 152268Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000152 AC: 38AN: 249940Hom.: 1 AF XY: 0.000133 AC XY: 18AN XY: 135374
GnomAD4 exome AF: 0.0000308 AC: 45AN: 1461620Hom.: 1 Cov.: 30 AF XY: 0.0000220 AC XY: 16AN XY: 727100
GnomAD4 genome AF: 0.000355 AC: 54AN: 152268Hom.: 0 Cov.: 33 AF XY: 0.000484 AC XY: 36AN XY: 74384
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 04, 2022 | The c.2169G>C (p.K723N) alteration is located in exon 11 (coding exon 11) of the SCARF1 gene. This alteration results from a G to C substitution at nucleotide position 2169, causing the lysine (K) at amino acid position 723 to be replaced by an asparagine (N). 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