rs200805356
Variant summary
Our verdict is Benign. Variant got -17 ACMG points: 0P and 17B. BP4_StrongBP6_Very_StrongBP7BS2
The NM_001008537.3(NEXMIF):c.4338G>A(p.Lys1446Lys) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000146 in 1,209,527 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 66 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_001008537.3 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -17 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
NEXMIF | ENST00000055682.12 | c.4338G>A | p.Lys1446Lys | synonymous_variant | Exon 3 of 4 | 1 | NM_001008537.3 | ENSP00000055682.5 | ||
NEXMIF | ENST00000616200.2 | c.4338G>A | p.Lys1446Lys | synonymous_variant | Exon 3 of 5 | 1 | ENSP00000480284.1 | |||
NEXMIF | ENST00000642681.2 | c.4338G>A | p.Lys1446Lys | synonymous_variant | Exon 3 of 3 | ENSP00000495800.1 |
Frequencies
GnomAD3 genomes AF: 0.0000628 AC: 7AN: 111441Hom.: 0 Cov.: 22 AF XY: 0.0000595 AC XY: 2AN XY: 33631
GnomAD3 exomes AF: 0.000115 AC: 21AN: 183300Hom.: 0 AF XY: 0.000133 AC XY: 9AN XY: 67780
GnomAD4 exome AF: 0.000154 AC: 169AN: 1098086Hom.: 0 Cov.: 31 AF XY: 0.000176 AC XY: 64AN XY: 363476
GnomAD4 genome AF: 0.0000628 AC: 7AN: 111441Hom.: 0 Cov.: 22 AF XY: 0.0000595 AC XY: 2AN XY: 33631
ClinVar
Submissions by phenotype
not specified Benign:1
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not provided Benign:1
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X-linked intellectual disability, Cantagrel type Benign:1
This variant has not been reported in the literature but is present in the Genome Aggregation Database (Highest reported MAF 0.01% (6/53144) including 2 hemizygotes (https://gnomad.broadinstitute.org/variant/X-74740219-C-T?dataset=gnomad_r3). This variant is present in ClinVar, with multiple labs classifying this variant as Likely Benign (Variation ID:435594). Evolutionary conservation and computational predictive tools for this variant are limited or unavailable. Of note, this variant is a silent variant and does not change the amino acid, reducing the probability that this variant is disease causing. In summary, data on this variant suggests that this variant does not cause disease but requires further evidence. Therefore, this variant is classified as likely benign. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at