rs1891110
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The ENST00000368898.8(FAM24B):c.5C>T(p.Pro2Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.546 in 1,608,986 control chromosomes in the GnomAD database, including 242,110 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
ENST00000368898.8 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
FAM24B | NM_152644.3 | c.5C>T | p.Pro2Leu | missense_variant | 3/4 | ENST00000368898.8 | NP_689857.2 | |
FAM24B-CUZD1 | NR_037915.1 | n.300-4291C>T | intron_variant, non_coding_transcript_variant | |||||
FAM24B | NM_001204364.1 | c.5C>T | p.Pro2Leu | missense_variant | 3/4 | NP_001191293.1 | ||
FAM24B | NR_037911.1 | n.300-1072C>T | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
FAM24B | ENST00000368898.8 | c.5C>T | p.Pro2Leu | missense_variant | 3/4 | 1 | NM_152644.3 | ENSP00000357894 | P1 | |
FAM24B | ENST00000368896.1 | c.5C>T | p.Pro2Leu | missense_variant | 3/4 | 2 | ENSP00000357892 | P1 | ||
FAM24B | ENST00000462859.5 | n.300-1072C>T | intron_variant, non_coding_transcript_variant | 2 |
Frequencies
GnomAD3 genomes AF: 0.541 AC: 82086AN: 151864Hom.: 22370 Cov.: 31
GnomAD3 exomes AF: 0.530 AC: 133068AN: 251268Hom.: 35760 AF XY: 0.531 AC XY: 72045AN XY: 135784
GnomAD4 exome AF: 0.547 AC: 796951AN: 1457006Hom.: 219707 Cov.: 32 AF XY: 0.545 AC XY: 395378AN XY: 725110
GnomAD4 genome AF: 0.541 AC: 82169AN: 151980Hom.: 22403 Cov.: 31 AF XY: 0.542 AC XY: 40301AN XY: 74290
ClinVar
Submissions by phenotype
not provided Benign:2
Benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jan 10, 2019 | This variant is associated with the following publications: (PMID: 29083408) - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at