chr3-161242621-C-T
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong
The NM_015938.5(NMD3):c.985C>T(p.Arg329Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000992 in 1,613,108 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_015938.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NMD3 | NM_015938.5 | c.985C>T | p.Arg329Cys | missense_variant | 11/16 | ENST00000351193.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NMD3 | ENST00000351193.7 | c.985C>T | p.Arg329Cys | missense_variant | 11/16 | 1 | NM_015938.5 | P1 | |
NMD3 | ENST00000472947.5 | c.985C>T | p.Arg329Cys | missense_variant | 11/17 | 1 | |||
NMD3 | ENST00000460469.1 | c.985C>T | p.Arg329Cys | missense_variant | 10/15 | 1 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000921 AC: 14AN: 151994Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000199 AC: 50AN: 251038Hom.: 1 AF XY: 0.000258 AC XY: 35AN XY: 135690
GnomAD4 exome AF: 0.0000999 AC: 146AN: 1460996Hom.: 2 Cov.: 31 AF XY: 0.000128 AC XY: 93AN XY: 726768
GnomAD4 genome ? AF: 0.0000920 AC: 14AN: 152112Hom.: 0 Cov.: 32 AF XY: 0.000121 AC XY: 9AN XY: 74342
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jun 02, 2023 | The c.985C>T (p.R329C) alteration is located in exon 11 (coding exon 10) of the NMD3 gene. This alteration results from a C to T substitution at nucleotide position 985, causing the arginine (R) at amino acid position 329 to be replaced by a cysteine (C). 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