rs2076530
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001304561.2(BTNL2):āc.1078A>Gā(p.Ser360Gly) variant causes a missense, splice region change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.436 in 1,605,698 control chromosomes in the GnomAD database, including 154,229 homozygotes. In-silico tool predicts a benign outcome for this variant. 16/21 in silico tools predict a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_001304561.2 missense, splice_region
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -12 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
BTNL2 | NM_001304561.2 | c.1078A>G | p.Ser360Gly | missense_variant, splice_region_variant | 5/8 | ENST00000454136.8 | |
TSBP1-AS1 | NR_136245.1 | n.303-9415T>C | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
BTNL2 | ENST00000454136.8 | c.1078A>G | p.Ser360Gly | missense_variant, splice_region_variant | 5/8 | 5 | NM_001304561.2 | P1 | |
TSBP1-AS1 | ENST00000645134.1 | n.627+5286T>C | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes AF: 0.402 AC: 61050AN: 152002Hom.: 12370 Cov.: 32
GnomAD3 exomes AF: 0.423 AC: 103271AN: 244188Hom.: 22391 AF XY: 0.422 AC XY: 56164AN XY: 133068
GnomAD4 exome AF: 0.439 AC: 638248AN: 1453578Hom.: 141857 Cov.: 32 AF XY: 0.437 AC XY: 315523AN XY: 722736
GnomAD4 genome AF: 0.401 AC: 61070AN: 152120Hom.: 12372 Cov.: 32 AF XY: 0.403 AC XY: 29967AN XY: 74350
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at