4-102885207-C-A
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 2P and 12B. PM2BP4_StrongBP6_Very_Strong
The NM_001100874.3(SLC9B1):c.*26G>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000125 in 1,609,040 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_001100874.3 3_prime_UTR
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CISD2 | NM_001008388.5 | c.104-9C>A | intron_variant | Intron 1 of 2 | ENST00000273986.10 | NP_001008389.1 | ||
SLC9B1 | NM_001100874.3 | c.*26G>T | 3_prime_UTR_variant | Exon 12 of 12 | NP_001094344.2 | |||
SLC9B1 | NR_047513.2 | n.1434G>T | non_coding_transcript_exon_variant | Exon 11 of 11 | ||||
SLC9B1 | NR_047515.2 | n.1296G>T | non_coding_transcript_exon_variant | Exon 11 of 11 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000664 AC: 101AN: 152218Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000167 AC: 42AN: 251370Hom.: 0 AF XY: 0.000177 AC XY: 24AN XY: 135864
GnomAD4 exome AF: 0.0000686 AC: 100AN: 1456704Hom.: 1 Cov.: 31 AF XY: 0.0000703 AC XY: 51AN XY: 725006
GnomAD4 genome AF: 0.000663 AC: 101AN: 152336Hom.: 0 Cov.: 32 AF XY: 0.000752 AC XY: 56AN XY: 74496
ClinVar
Submissions by phenotype
CISD2-related disorder Benign:1
This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -
not provided Benign:1
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Wolfram syndrome 2 Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at