15-29268942-T-A
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_138704.4(NSMCE3):c.764A>T(p.Asn255Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00196 in 1,614,172 control chromosomes in the GnomAD database, including 59 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_138704.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NSMCE3 | NM_138704.4 | c.764A>T | p.Asn255Ile | missense_variant | 1/1 | ENST00000332303.6 | |
ENTREP2 | NM_015307.2 | c.277-16464A>T | intron_variant | ENST00000261275.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NSMCE3 | ENST00000332303.6 | c.764A>T | p.Asn255Ile | missense_variant | 1/1 | NM_138704.4 | P1 | ||
ENTREP2 | ENST00000261275.5 | c.277-16464A>T | intron_variant | 5 | NM_015307.2 | P1 | |||
ENTREP2 | ENST00000560082.1 | c.-12-16464A>T | intron_variant | 4 |
Frequencies
GnomAD3 genomes AF: 0.0104 AC: 1577AN: 152160Hom.: 27 Cov.: 32
GnomAD3 exomes AF: 0.00262 AC: 659AN: 251474Hom.: 14 AF XY: 0.00189 AC XY: 257AN XY: 135916
GnomAD4 exome AF: 0.00108 AC: 1575AN: 1461894Hom.: 32 Cov.: 30 AF XY: 0.000920 AC XY: 669AN XY: 727248
GnomAD4 genome AF: 0.0104 AC: 1584AN: 152278Hom.: 27 Cov.: 32 AF XY: 0.00967 AC XY: 720AN XY: 74456
ClinVar
Submissions by phenotype
not provided Benign:2
Benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jan 31, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at