1-15660482-A-T
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_006511.3(RSC1A1):c.614A>T(p.Asn205Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00274 in 1,614,096 control chromosomes in the GnomAD database, including 10 homozygotes. 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 (★).
Frequency
Consequence
NM_006511.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
RSC1A1 | ENST00000345034.2 | c.614A>T | p.Asn205Ile | missense_variant | Exon 1 of 1 | 6 | NM_006511.3 | ENSP00000341963.1 | ||
DDI2 | ENST00000480945.6 | c.*692A>T | 3_prime_UTR_variant | Exon 10 of 10 | 2 | NM_032341.5 | ENSP00000417748.1 |
Frequencies
GnomAD3 genomes AF: 0.00194 AC: 295AN: 152254Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.00190 AC: 475AN: 250534Hom.: 0 AF XY: 0.00189 AC XY: 256AN XY: 135394
GnomAD4 exome AF: 0.00283 AC: 4131AN: 1461724Hom.: 10 Cov.: 32 AF XY: 0.00273 AC XY: 1988AN XY: 727138
GnomAD4 genome AF: 0.00194 AC: 295AN: 152372Hom.: 0 Cov.: 33 AF XY: 0.00166 AC XY: 124AN XY: 74522
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.614A>T (p.N205I) alteration is located in exon 1 (coding exon 1) of the RSC1A1 gene. This alteration results from a A to T substitution at nucleotide position 614, causing the asparagine (N) at amino acid position 205 to be replaced by an isoleucine (I). 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