chr4-102885256-C-T
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The ENST00000394789.7(SLC9B1):c.1405G>A(p.Glu469Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000204 in 1,613,928 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/15 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★). Synonymous variant affecting the same amino acid position (i.e. E469E) has been classified as Uncertain significance.
Frequency
Consequence
ENST00000394789.7 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CISD2 | NM_001008388.5 | c.144C>T | p.Leu48= | synonymous_variant | 2/3 | ENST00000273986.10 | |
SLC9B1 | NM_001100874.3 | c.1405G>A | p.Glu469Lys | missense_variant | 12/12 | ||
SLC9B1 | NR_047513.2 | n.1385G>A | non_coding_transcript_exon_variant | 11/11 | |||
SLC9B1 | NR_047515.2 | n.1247G>A | non_coding_transcript_exon_variant | 11/11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CISD2 | ENST00000273986.10 | c.144C>T | p.Leu48= | synonymous_variant | 2/3 | 1 | NM_001008388.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000723 AC: 11AN: 152150Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000159 AC: 4AN: 251418Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135894
GnomAD4 exome AF: 0.0000151 AC: 22AN: 1461778Hom.: 0 Cov.: 32 AF XY: 0.0000193 AC XY: 14AN XY: 727186
GnomAD4 genome ? AF: 0.0000723 AC: 11AN: 152150Hom.: 0 Cov.: 32 AF XY: 0.0000807 AC XY: 6AN XY: 74320
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 11, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at