chr11-71796123-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The ENST00000524714.1(ALG1L9P):n.286G>A variant causes a splice region, non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000013 in 1,613,770 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 1/1 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
ENST00000524714.1 splice_region, non_coding_transcript_exon
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 rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ALG1L9P | NR_073388.1 | n.699G>A | splice_region_variant, non_coding_transcript_exon_variant | Exon 4 of 4 | ||||
FAM86C1P | XR_004643250.2 | n.872C>T | non_coding_transcript_exon_variant | Exon 7 of 8 | ||||
ALG1L9P | NR_073386.1 | n.697-869G>A | intron_variant | Intron 3 of 3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ENSG00000291186 | ENST00000346333.11 | n.322C>T | non_coding_transcript_exon_variant | Exon 3 of 4 | 1 | |||||
ENSG00000291186 | ENST00000510443.6 | n.498C>T | non_coding_transcript_exon_variant | Exon 4 of 5 | 1 | |||||
ENSG00000291186 | ENST00000526393.5 | n.478C>T | non_coding_transcript_exon_variant | Exon 5 of 5 | 1 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152270Hom.: 0 Cov.: 36
GnomAD3 exomes AF: 0.0000199 AC: 5AN: 251178Hom.: 0 AF XY: 0.0000221 AC XY: 3AN XY: 135742
GnomAD4 exome AF: 0.0000137 AC: 20AN: 1461500Hom.: 0 Cov.: 53 AF XY: 0.0000138 AC XY: 10AN XY: 727042
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152270Hom.: 0 Cov.: 36 AF XY: 0.00 AC XY: 0AN XY: 74396
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.368C>T (p.P123L) alteration is located in exon 4 (coding exon 4) of the FAM86C1 gene. This alteration results from a C to T substitution at nucleotide position 368, causing the proline (P) at amino acid position 123 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