NM_014208.3:c.1060C>T
Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP6BS1BS2
The NM_014208.3(DSPP):c.1060C>T(p.Arg354Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00497 in 1,613,718 control chromosomes in the GnomAD database, including 39 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_014208.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -13 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00369 AC: 561AN: 152060Hom.: 3 Cov.: 33
GnomAD3 exomes AF: 0.00438 AC: 1080AN: 246612Hom.: 4 AF XY: 0.00461 AC XY: 620AN XY: 134496
GnomAD4 exome AF: 0.00510 AC: 7451AN: 1461540Hom.: 36 Cov.: 35 AF XY: 0.00523 AC XY: 3805AN XY: 727068
GnomAD4 genome AF: 0.00369 AC: 562AN: 152178Hom.: 3 Cov.: 33 AF XY: 0.00391 AC XY: 291AN XY: 74400
ClinVar
Submissions by phenotype
not provided Benign:5
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DSPP: BP4, BS2 -
not specified Benign:3
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Inborn genetic diseases Uncertain:1
The c.1060C>T (p.R354C) alteration is located in exon 4 (coding exon 3) of the DSPP gene. This alteration results from a C to T substitution at nucleotide position 1060, causing the arginine (R) at amino acid position 354 to be replaced by a cysteine (C). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -
Deafness, autosomal dominant 39, with dentinogenesis imperfecta 1 Uncertain:1
This variant was determined to be of uncertain significance according to ACMG Guidelines, 2015 [PMID:25741868]. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at