5-181050232-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_152547.5(BTNL9):c.599C>T(p.Ala200Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000137 in 1,461,810 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_152547.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
BTNL9 | ENST00000327705.14 | c.599C>T | p.Ala200Val | missense_variant | Exon 4 of 11 | 1 | NM_152547.5 | ENSP00000330200.9 | ||
BTNL9 | ENST00000376841.6 | c.599C>T | p.Ala200Val | missense_variant | Exon 4 of 11 | 1 | ENSP00000366037.2 | |||
BTNL9 | ENST00000515271.1 | c.392C>T | p.Ala131Val | missense_variant | Exon 3 of 5 | 2 | ENSP00000427345.1 | |||
BTNL9 | ENST00000491209.5 | n.599C>T | non_coding_transcript_exon_variant | Exon 4 of 7 | 2 | ENSP00000425424.1 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 exomes AF: 0.00000398 AC: 1AN: 251460Hom.: 0 AF XY: 0.00000736 AC XY: 1AN XY: 135916
GnomAD4 exome AF: 0.00000137 AC: 2AN: 1461810Hom.: 0 Cov.: 31 AF XY: 0.00000138 AC XY: 1AN XY: 727186
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.599C>T (p.A200V) alteration is located in exon 4 (coding exon 3) of the BTNL9 gene. This alteration results from a C to T substitution at nucleotide position 599, causing the alanine (A) at amino acid position 200 to be replaced by a valine (V). 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