chr2-40160780-T-C
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_021097.5(SLC8A1):c.2254A>G(p.Ile752Val) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000806 in 1,613,050 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Synonymous variant affecting the same amino acid position (i.e. I752I) has been classified as Likely benign.
Frequency
Consequence
NM_021097.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLC8A1 | NM_021097.5 | c.2254A>G | p.Ile752Val | missense_variant | 9/11 | ENST00000332839.9 | |
SLC8A1-AS1 | NR_038441.1 | n.121+55818T>C | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC8A1 | ENST00000332839.9 | c.2254A>G | p.Ile752Val | missense_variant | 9/11 | 1 | NM_021097.5 | P4 | |
SLC8A1-AS1 | ENST00000599740.1 | n.74-90904T>C | intron_variant, non_coding_transcript_variant | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.0000460 AC: 7AN: 152138Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000797 AC: 2AN: 250994Hom.: 0 AF XY: 0.0000147 AC XY: 2AN XY: 135632
GnomAD4 exome AF: 0.00000411 AC: 6AN: 1460912Hom.: 0 Cov.: 30 AF XY: 0.00000413 AC XY: 3AN XY: 726790
GnomAD4 genome ? AF: 0.0000460 AC: 7AN: 152138Hom.: 0 Cov.: 32 AF XY: 0.0000404 AC XY: 3AN XY: 74328
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | May 27, 2022 | The c.2254A>G (p.I752V) alteration is located in exon 8 (coding exon 8) of the SLC8A1 gene. This alteration results from a A to G substitution at nucleotide position 2254, causing the isoleucine (I) at amino acid position 752 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