NM_007214.5:c.340-9T>C
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_007214.5(SEC63):c.340-9T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_007214.5 intron
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 rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SEC63 | NM_007214.5 | c.340-9T>C | intron_variant | Intron 3 of 20 | ENST00000369002.9 | NP_009145.1 | ||
SEC63 | XM_047418130.1 | c.172-9T>C | intron_variant | Intron 3 of 20 | XP_047274086.1 | |||
SEC63 | XM_047418131.1 | c.-81-9T>C | intron_variant | Intron 2 of 19 | XP_047274087.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SEC63 | ENST00000369002.9 | c.340-9T>C | intron_variant | Intron 3 of 20 | 1 | NM_007214.5 | ENSP00000357998.4 | |||
SEC63 | ENST00000429168.1 | c.172-9T>C | intron_variant | Intron 3 of 7 | 5 | ENSP00000403144.1 | ||||
SEC63 | ENST00000484803.5 | n.262-9T>C | intron_variant | Intron 3 of 6 | 2 |
Frequencies
GnomAD3 genomes AF: 0.00781 AC: 24AN: 3072Hom.: 0 Cov.: 0
GnomAD3 exomes AF: 0.000361 AC: 63AN: 174382Hom.: 1 AF XY: 0.000317 AC XY: 30AN XY: 94770
GnomAD4 exome AF: 0.00282 AC: 194AN: 68712Hom.: 2 Cov.: 0 AF XY: 0.00280 AC XY: 95AN XY: 33880
GnomAD4 genome AF: 0.00810 AC: 25AN: 3088Hom.: 0 Cov.: 0 AF XY: 0.00927 AC XY: 14AN XY: 1510
ClinVar
Submissions by phenotype
not provided Benign:2
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not specified Benign:1
Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or databases. Disclaimer: This variant has not undergone full assessment. The following are preliminary notes: No change to splice consensus -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at