chr12-57078697-G-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001130963.2(NEMP1):c.49C>T(p.Pro17Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000886 in 1,613,236 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001130963.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NEMP1 | NM_001130963.2 | c.49C>T | p.Pro17Ser | missense_variant | 1/9 | ENST00000300128.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NEMP1 | ENST00000300128.9 | c.49C>T | p.Pro17Ser | missense_variant | 1/9 | 1 | NM_001130963.2 | P1 | |
NEMP1 | ENST00000379391.7 | c.49C>T | p.Pro17Ser | missense_variant | 1/8 | 1 | |||
NEMP1 | ENST00000554340.1 | c.49C>T | p.Pro17Ser | missense_variant, NMD_transcript_variant | 1/8 | 1 | |||
NEMP1 | ENST00000553654.1 | n.114-5785C>T | intron_variant, non_coding_transcript_variant | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.000112 AC: 17AN: 152148Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000161 AC: 40AN: 249122Hom.: 0 AF XY: 0.000178 AC XY: 24AN XY: 135054
GnomAD4 exome AF: 0.0000862 AC: 126AN: 1461088Hom.: 1 Cov.: 30 AF XY: 0.0000812 AC XY: 59AN XY: 726838
GnomAD4 genome ? AF: 0.000112 AC: 17AN: 152148Hom.: 0 Cov.: 32 AF XY: 0.0000807 AC XY: 6AN XY: 74342
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jul 19, 2022 | The c.49C>T (p.P17S) alteration is located in exon 1 (coding exon 1) of the NEMP1 gene. This alteration results from a C to T substitution at nucleotide position 49, causing the proline (P) at amino acid position 17 to be replaced by a serine (S). 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