rs34157476
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBS1BS2
The NM_007190.4(SEC23IP):c.721G>T(p.Ala241Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0176 in 1,614,088 control chromosomes in the GnomAD database, including 315 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Consequence
NM_007190.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -12 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SEC23IP | NM_007190.4 | c.721G>T | p.Ala241Ser | missense_variant | 3/19 | ENST00000369075.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SEC23IP | ENST00000369075.8 | c.721G>T | p.Ala241Ser | missense_variant | 3/19 | 1 | NM_007190.4 | P4 | |
SEC23IP | ENST00000705471.1 | c.721G>T | p.Ala241Ser | missense_variant | 3/19 | A1 | |||
SEC23IP | ENST00000442952.1 | c.19G>T | p.Ala7Ser | missense_variant | 1/2 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.0151 AC: 2292AN: 152134Hom.: 22 Cov.: 32
GnomAD3 exomes AF: 0.0157 AC: 3947AN: 251370Hom.: 45 AF XY: 0.0161 AC XY: 2187AN XY: 135862
GnomAD4 exome AF: 0.0179 AC: 26118AN: 1461838Hom.: 293 Cov.: 31 AF XY: 0.0177 AC XY: 12862AN XY: 727222
GnomAD4 genome ? AF: 0.0150 AC: 2288AN: 152250Hom.: 22 Cov.: 32 AF XY: 0.0154 AC XY: 1145AN XY: 74436
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at