4-122742606-T-G
Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP6BS1BS2
The NM_152618.3(BBS12):āc.714T>Gā(p.Asn238Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00151 in 1,614,212 control chromosomes in the GnomAD database, including 29 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_152618.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -13 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
BBS12 | NM_152618.3 | c.714T>G | p.Asn238Lys | missense_variant | Exon 2 of 2 | ENST00000314218.8 | NP_689831.2 | |
BBS12 | NM_001178007.2 | c.714T>G | p.Asn238Lys | missense_variant | Exon 3 of 3 | NP_001171478.1 | ||
BBS12 | XM_011531680.3 | c.714T>G | p.Asn238Lys | missense_variant | Exon 2 of 2 | XP_011529982.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
BBS12 | ENST00000314218.8 | c.714T>G | p.Asn238Lys | missense_variant | Exon 2 of 2 | 1 | NM_152618.3 | ENSP00000319062.3 | ||
BBS12 | ENST00000542236.5 | c.714T>G | p.Asn238Lys | missense_variant | Exon 3 of 3 | 2 | ENSP00000438273.1 | |||
BBS12 | ENST00000433287.1 | c.*141T>G | downstream_gene_variant | 2 | ENSP00000398912.1 |
Frequencies
GnomAD3 genomes AF: 0.00792 AC: 1205AN: 152224Hom.: 13 Cov.: 33
GnomAD3 exomes AF: 0.00196 AC: 493AN: 251308Hom.: 6 AF XY: 0.00149 AC XY: 203AN XY: 135832
GnomAD4 exome AF: 0.000843 AC: 1232AN: 1461870Hom.: 16 Cov.: 32 AF XY: 0.000748 AC XY: 544AN XY: 727234
GnomAD4 genome AF: 0.00794 AC: 1209AN: 152342Hom.: 13 Cov.: 33 AF XY: 0.00764 AC XY: 569AN XY: 74500
ClinVar
Submissions by phenotype
Bardet-Biedl syndrome 1 Benign:3
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Bardet-Biedl syndrome 12 Uncertain:1Benign:1
This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). No publications were found based on this search. Allele frequency data from public databases did not allow this variant to be ruled in or out of causing disease. Therefore, this variant is classified as a variant of unknown significance. -
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not specified Benign:1
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Bardet-Biedl syndrome Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at