12-56923941-G-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_148897.3(SDR9C7):c.834C>A(p.Asn278Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000115 in 1,613,966 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★★).
Frequency
Consequence
NM_148897.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000138 AC: 21AN: 152190Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000219 AC: 55AN: 251288Hom.: 0 AF XY: 0.000184 AC XY: 25AN XY: 135814
GnomAD4 exome AF: 0.000112 AC: 164AN: 1461776Hom.: 0 Cov.: 31 AF XY: 0.000117 AC XY: 85AN XY: 727204
GnomAD4 genome AF: 0.000138 AC: 21AN: 152190Hom.: 0 Cov.: 32 AF XY: 0.000188 AC XY: 14AN XY: 74356
ClinVar
Submissions by phenotype
not provided Uncertain:2
- -
Has not been previously published as pathogenic or benign to our knowledge; In silico analysis supports that this missense variant does not alter protein structure/function -
Inborn genetic diseases Uncertain:1
The c.834C>A (p.N278K) alteration is located in exon 4 (coding exon 4) of the SDR9C7 gene. This alteration results from a C to A substitution at nucleotide position 834, causing the asparagine (N) at amino acid position 278 to be replaced by a lysine (K). 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