chr1-109316860-G-A
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_002959.7(SORT1):c.2240C>T(p.Pro747Leu) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000015 in 1,601,262 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Synonymous variant affecting the same amino acid position (i.e. P747P) has been classified as Likely benign.
Frequency
Consequence
NM_002959.7 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SORT1 | NM_002959.7 | c.2240C>T | p.Pro747Leu | missense_variant | 17/20 | ENST00000256637.8 | |
SORT1 | NM_001205228.2 | c.1829C>T | p.Pro610Leu | missense_variant | 17/20 | ||
SORT1 | XM_005271100.3 | c.2237C>T | p.Pro746Leu | missense_variant | 17/20 | ||
SORT1 | XM_005271101.4 | c.1832C>T | p.Pro611Leu | missense_variant | 17/20 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SORT1 | ENST00000256637.8 | c.2240C>T | p.Pro747Leu | missense_variant | 17/20 | 1 | NM_002959.7 | P1 | |
SORT1 | ENST00000538502.5 | c.1829C>T | p.Pro610Leu | missense_variant | 17/20 | 2 | |||
SORT1 | ENST00000485149.1 | n.68C>T | non_coding_transcript_exon_variant | 1/3 | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.0000395 AC: 6AN: 152008Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000611 AC: 15AN: 245586Hom.: 0 AF XY: 0.0000603 AC XY: 8AN XY: 132646
GnomAD4 exome AF: 0.0000124 AC: 18AN: 1449254Hom.: 0 Cov.: 28 AF XY: 0.0000111 AC XY: 8AN XY: 721402
GnomAD4 genome ? AF: 0.0000395 AC: 6AN: 152008Hom.: 0 Cov.: 31 AF XY: 0.0000539 AC XY: 4AN XY: 74234
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 12, 2024 | The c.2240C>T (p.P747L) alteration is located in exon 17 (coding exon 17) of the SORT1 gene. This alteration results from a C to T substitution at nucleotide position 2240, causing the proline (P) at amino acid position 747 to be replaced by a leucine (L). 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