chr4-103031712-G-C
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_178833.7(SLC9B2):āc.1243C>Gā(p.Pro415Ala) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00298 in 1,611,908 control chromosomes in the GnomAD database, including 59 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ā ).
Frequency
Consequence
NM_178833.7 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SLC9B2 | NM_178833.7 | c.1243C>G | p.Pro415Ala | missense_variant | 10/12 | ENST00000394785.9 | NP_849155.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SLC9B2 | ENST00000394785.9 | c.1243C>G | p.Pro415Ala | missense_variant | 10/12 | 2 | NM_178833.7 | ENSP00000378265 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0104 AC: 1589AN: 152060Hom.: 19 Cov.: 32
GnomAD3 exomes AF: 0.00369 AC: 924AN: 250410Hom.: 11 AF XY: 0.00306 AC XY: 414AN XY: 135354
GnomAD4 exome AF: 0.00219 AC: 3202AN: 1459730Hom.: 40 Cov.: 30 AF XY: 0.00216 AC XY: 1565AN XY: 726204
GnomAD4 genome AF: 0.0105 AC: 1596AN: 152178Hom.: 19 Cov.: 32 AF XY: 0.00993 AC XY: 739AN XY: 74412
ClinVar
Submissions by phenotype
not provided Benign:2
Benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jan 30, 2018 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at